diff --git a/docs/reference/docfx-cli-reference/docfx-clean.md b/docs/reference/docfx-cli-reference/docfx-clean.md
new file mode 100644
index 00000000000..0b1dc8d0d15
--- /dev/null
+++ b/docs/reference/docfx-cli-reference/docfx-clean.md
@@ -0,0 +1,44 @@
+# docfx clean
+
+## Name
+
+`docfx clean [OPTIONS]` - Cleanup temporary files that are generated by docfx.
+
+## Usage
+
+```pwsh
+docfx clean [OPTIONS]
+```
+
+Run `docfx clean --help` or `docfx -h` to get a list of all available options.
+
+## Arguments
+
+- `[config]` <span class="badge text-bg-primary">optional</span>
+
+  Specify the path to the docfx configuration file.
+  By default, the `docfx.json' file path is used.
+
+## Options
+
+- **-h|--help**
+
+  Prints help information
+
+- **--dryRun**
+
+  If set to true, Skip actual file deletion.
+
+## Examples
+
+- Cleanup temporary files that are generated by docfx.
+
+```pwsh
+docfx clean
+```
+
+- Print a list of the files expected to be deleted.
+
+```pwsh
+docfx clean --dryRun --verbose
+```
diff --git a/docs/reference/docfx-cli-reference/overview.md b/docs/reference/docfx-cli-reference/overview.md
index 202e75618e3..31598d00f39 100644
--- a/docs/reference/docfx-cli-reference/overview.md
+++ b/docs/reference/docfx-cli-reference/overview.md
@@ -36,6 +36,7 @@ Generating offline documentation such as **PDF** is also supported.
 | [docfx build](docfx-build.md)       | Generate static site contents from input files.                            |
 | [docfx pdf](docfx-pdf.md)           | Generate pdf file.                                                         |
 | [docfx serve](docfx-serve.md)       | Host a local static website.                                               |
+| [docfx clean](docfx-clean.md)       | Cleanup temporary files that are generated by docfx.                       |
 | [docfx init](docfx-init.md)         | Generate an initial docfx.json following the instructions.                 |
 | [docfx template](docfx-template.md) | List available templates or export template files.                         |
 | [docfx download](docfx-download.md) | Download remote xref map file and create an xref archive(`.zip`) in local. |
diff --git a/docs/reference/docfx-cli-reference/toc.yml b/docs/reference/docfx-cli-reference/toc.yml
index 92548146a54..2400e3300da 100644
--- a/docs/reference/docfx-cli-reference/toc.yml
+++ b/docs/reference/docfx-cli-reference/toc.yml
@@ -4,6 +4,7 @@
 - href: docfx-build.md
 - href: docfx-pdf.md
 - href: docfx-serve.md
+- href: docfx-clean.md
 - href: docfx-init.md
 - href: docfx-template.md
 - href: docfx-download.md
diff --git a/src/Docfx.App/Config/CleanJsonConfig.cs b/src/Docfx.App/Config/CleanJsonConfig.cs
new file mode 100644
index 00000000000..ff883a1ff4e
--- /dev/null
+++ b/src/Docfx.App/Config/CleanJsonConfig.cs
@@ -0,0 +1,19 @@
+// Licensed to the .NET Foundation under one or more agreements.
+// The .NET Foundation licenses this file to you under the MIT license.
+
+using System.Text.Json.Serialization;
+using Newtonsoft.Json;
+
+#nullable enable
+
+namespace Docfx;
+
+internal class CleanJsonConfig
+{
+    /// <summary>
+    /// If set to true, skip file/directory delete operations.
+    /// </summary>
+    [JsonProperty("dryRun")]
+    [JsonPropertyName("dryRun")]
+    public bool? DryRun { get; set; }
+}
diff --git a/src/Docfx.App/Models/RunCleanContext.cs b/src/Docfx.App/Models/RunCleanContext.cs
new file mode 100644
index 00000000000..d7a1617556a
--- /dev/null
+++ b/src/Docfx.App/Models/RunCleanContext.cs
@@ -0,0 +1,57 @@
+// Licensed to the .NET Foundation under one or more agreements.
+// The .NET Foundation licenses this file to you under the MIT license.
+
+namespace Docfx;
+
+#nullable enable
+
+/// <summary>
+/// Clean command context class to execute <see cref="RunClean.Exec(RunCleanContext, CancellationToken)/>.
+/// </summary>
+internal class RunCleanContext
+{
+    private int _deletedFilesCount = 0;
+    private int _skippedFilesCount = 0;
+
+    /// <summary>
+    /// config file directory.
+    /// `docfx clean`cleanup files/directories under this
+    /// </summary>
+    public required string ConfigDirectory { get; init; }
+
+    /// <summary>
+    /// Output directory of `docfx build` command.
+    /// </summary>
+    public required string BuildOutputDirectory { get; init; }
+
+    /// <summary>
+    /// Output directories of `docfx metadata` command.
+    /// </summary>
+    public required string[] MetadataOutputDirectories { get; init; }
+
+    /// <summary>
+    /// If enabled. Skip files/directories delete operations.
+    /// </summary>
+    public bool DryRun { get; init; }
+
+    /// <summary>
+    /// Gets deleted files count.
+    /// </summary>
+    /// <remarks>
+    public int DeletedFilesCount => _deletedFilesCount;
+
+    /// <summary>
+    /// Gets skipped files count.
+    /// </summary>
+    public int SkippedFilesCount => _skippedFilesCount;
+
+    /// <summary>
+    /// Increment <see cref="DeletedFilesCount"/>.
+    /// </summary>
+    public void IncrementDeletedFilesCount() => Interlocked.Increment(ref _deletedFilesCount);
+
+    /// <summary>
+    /// Increment <see cref="SkippedFilesCount"/>.
+    /// </summary>
+    public void IncrementSkippedFilesCount() => Interlocked.Increment(ref _skippedFilesCount);
+}
diff --git a/src/Docfx.App/RunClean.cs b/src/Docfx.App/RunClean.cs
new file mode 100644
index 00000000000..4dd1e9d8cec
--- /dev/null
+++ b/src/Docfx.App/RunClean.cs
@@ -0,0 +1,176 @@
+// Licensed to the .NET Foundation under one or more agreements.
+// The .NET Foundation licenses this file to you under the MIT license.
+
+using System.Diagnostics;
+using Docfx.Common;
+
+#nullable enable
+
+namespace Docfx;
+
+/// <summary>
+/// Helper class to cleanup docfx temporary files.
+/// </summary>
+internal static class RunClean
+{
+    private const string SearchPattern = "*";
+    private static readonly EnumerationOptions DefaultEnumerationOptions = new()
+    {
+        MatchType = MatchType.Simple,
+        RecurseSubdirectories = false,
+        IgnoreInaccessible = true,
+    };
+
+    private static readonly StringComparison PathStringComparer = PathUtility.IsPathCaseInsensitive()
+                                                                      ? StringComparison.OrdinalIgnoreCase
+                                                                      : StringComparison.Ordinal;
+
+    /// <summary>
+    /// Cleanup docfx temporary files/directories.
+    /// </summary>
+    public static void Exec(RunCleanContext context, CancellationToken cancellationToken = default)
+    {
+        Logger.LogInfo("Clean operation started...");
+
+        var startingTimestamp = Stopwatch.GetTimestamp();
+
+        // Cleanup build output directory.
+        var buildOutputDir = context.BuildOutputDirectory;
+        if (!string.IsNullOrEmpty(buildOutputDir))
+        {
+            Logger.LogInfo($"Running clean operation on build output directory: {buildOutputDir}");
+            CleanDirectoryContents(buildOutputDir, context, cancellationToken);
+        }
+
+        // Cleanup metadata output directories.
+        foreach (var metadataOutputDir in context.MetadataOutputDirectories)
+        {
+            Logger.LogInfo($"Running clean operation on metadata output directory: {metadataOutputDir}");
+            CleanDirectoryContents(metadataOutputDir, context, cancellationToken);
+        }
+
+        var elapsedSec = Stopwatch.GetElapsedTime(startingTimestamp).TotalSeconds;
+        Logger.LogInfo($"Clean: {context.DeletedFilesCount} files are deleted, {context.SkippedFilesCount} files are skipped.");
+    }
+
+    /// <summary>
+    /// Delete specified directory contents.
+    /// </summary>
+    private static void CleanDirectoryContents(string directoryPath, RunCleanContext context, CancellationToken cancellationToken = default)
+    {
+        Debug.Assert(Path.IsPathFullyQualified(directoryPath));
+
+        if (!IsUnderConfigDirectoryPath(directoryPath, context.ConfigDirectory))
+        {
+            Logger.LogWarning($"Clean operation is not supported if the output directory is not located within a base directory that contains a `docfx.json`. path: {Path.GetFullPath(directoryPath)}");
+            return;
+        }
+
+        var dirInfo = new DirectoryInfo(directoryPath);
+        if (!dirInfo.Exists)
+            return; // Skip if specified path is not exists.
+
+        var configDirectory = context.ConfigDirectory;
+
+        // Delete sub directories
+        foreach (var subDirInfo in dirInfo.EnumerateDirectories(SearchPattern, DefaultEnumerationOptions))
+        {
+            cancellationToken.ThrowIfCancellationRequested();
+            DeleteDirectoryCore(subDirInfo, context, cancellationToken);
+        }
+
+        // Delete directory files
+        foreach (var fileInfo in dirInfo.EnumerateFiles(SearchPattern, DefaultEnumerationOptions))
+        {
+            cancellationToken.ThrowIfCancellationRequested();
+            DeleteFileCore(fileInfo, context);
+        }
+    }
+
+    /// <summary>
+    /// Delete specified directory recursively.
+    /// </summary>
+    private static void DeleteDirectoryCore(DirectoryInfo dirInfo, RunCleanContext context, CancellationToken cancellationToken)
+    {
+        // Skip directory deletion, if specified directory have LinkTarget (SymbolicLink/DirectoryJunction).
+        // Because it might cause unexpected deletion of file/directory or it might cause infinite loop.
+        if (dirInfo.LinkTarget != null)
+        {
+            Logger.LogWarning("Enumeration of directory contents is skipped. Because it has LinkTarget. Path: " + dirInfo.FullName);
+            return;
+        }
+
+        // Delete sub directories
+        foreach (var subDirInfo in dirInfo.EnumerateDirectories(SearchPattern, DefaultEnumerationOptions))
+        {
+            cancellationToken.ThrowIfCancellationRequested();
+            DeleteDirectoryCore(subDirInfo, context, cancellationToken);
+        }
+
+        // Delete files
+        foreach (var fileInfo in dirInfo.EnumerateFiles(SearchPattern, DefaultEnumerationOptions))
+        {
+            cancellationToken.ThrowIfCancellationRequested();
+            DeleteFileCore(fileInfo, context);
+        }
+
+        if (context.DryRun)
+            return;
+
+        // Try to delete root directory if there are no remaining files.
+        if (dirInfo.GetFileSystemInfos("*", DefaultEnumerationOptions).Length == 0)
+        {
+            try
+            {
+                dirInfo.Delete(recursive: false);
+            }
+            catch
+            {
+                Logger.LogWarning("Skipped (Failed to delete): " + dirInfo.FullName);
+                // Ignore exception. (File is being used by another process, has no permissions, or has readonly attribute)
+            }
+        }
+    }
+
+    private static void DeleteFileCore(FileInfo fileInfo, RunCleanContext context)
+    {
+        if (context.DryRun)
+        {
+            Logger.LogVerbose("Skipped: " + fileInfo.FullName);
+            context.IncrementSkippedFilesCount();
+            return;
+        }
+
+        if (fileInfo.LinkTarget != null)
+        {
+            Logger.LogWarning("File delete operation is skipped. Because it has LinkTarget. Path: " + fileInfo.FullName);
+            context.IncrementSkippedFilesCount();
+            return;
+        }
+
+        try
+        {
+            fileInfo.Delete();
+            context.IncrementDeletedFilesCount();
+        }
+        catch
+        {
+            // File is being used by another process, has no permissions, or has readonly attribute.
+            context.IncrementSkippedFilesCount();
+            Logger.LogWarning("Skipped (Failed to delete): " + fileInfo.FullName);
+        }
+    }
+
+    private static bool IsUnderConfigDirectoryPath(string targetPath, string basePath)
+    {
+        // Normalize paths
+        basePath = Path.GetFullPath(basePath).TrimEnd(Path.DirectorySeparatorChar);
+        targetPath = Path.GetFullPath(targetPath);
+
+        // Try to append directory separator for string comparison.
+        if (!targetPath.EndsWith(Path.DirectorySeparatorChar))
+            targetPath += Path.DirectorySeparatorChar;
+
+        return targetPath.StartsWith(basePath, PathStringComparer);
+    }
+}
diff --git a/src/docfx/Models/CleanCommand.cs b/src/docfx/Models/CleanCommand.cs
new file mode 100644
index 00000000000..30355e8cddd
--- /dev/null
+++ b/src/docfx/Models/CleanCommand.cs
@@ -0,0 +1,70 @@
+// Licensed to the .NET Foundation under one or more agreements.
+// The .NET Foundation licenses this file to you under the MIT license.
+
+using Spectre.Console.Cli;
+
+#nullable enable
+
+namespace Docfx;
+
+internal class CleanCommand : Command<CleanCommandOptions>
+{
+    public override int Execute(CommandContext context, CleanCommandOptions settings, CancellationToken cancellationToken)
+    {
+        return CommandHelper.Run(settings, () =>
+        {
+            // Gets docfx config path.
+            var configPath = string.IsNullOrEmpty(settings.ConfigFile)
+                               ? DataContracts.Common.Constants.ConfigFileName
+                               : settings.ConfigFile!;
+            configPath = Path.GetFullPath(configPath);
+
+            // Load configs
+            var (config, baseDirectory) = Docset.GetConfig(configPath);
+
+            // Gets output directories
+            var buildOutputDirectory = GetBuildOutputDirectory(config, baseDirectory);
+            var metadataOutputDirectories = GetMetadataOutputDirectories(config, baseDirectory);
+
+            RunClean.Exec(new RunCleanContext
+            {
+                ConfigDirectory = Path.GetDirectoryName(configPath)!,
+                BuildOutputDirectory = buildOutputDirectory,
+                MetadataOutputDirectories = metadataOutputDirectories,
+                DryRun = settings.DryRun,
+            });
+        });
+    }
+
+    /// <summary>
+    /// Gets output directory of `docfx build` command.
+    /// </summary>
+    internal static string GetBuildOutputDirectory(DocfxConfig config, string baseDirectory)
+    {
+        var buildConfig = config.build;
+        if (buildConfig == null)
+            return "";
+
+        // Combine path
+        var outputDirectory = Path.Combine(baseDirectory, buildConfig.Output ?? buildConfig.Dest ?? "");
+
+        // Normalize to full path 
+        return Path.GetFullPath(outputDirectory);
+    }
+
+    /// <summary>
+    /// Gets output directories of `docfx metadata` command.
+    /// </summary>
+    internal static string[] GetMetadataOutputDirectories(DocfxConfig config, string baseDirectory)
+    {
+        var metadataConfig = config.metadata;
+        if (metadataConfig == null)
+            return [];
+
+        return metadataConfig.Select(x =>
+        {
+            var outputDirectory = Path.Combine(baseDirectory, x.Output ?? x.Dest ?? "");
+            return Path.GetFullPath(outputDirectory);
+        }).ToArray();
+    }
+}
diff --git a/src/docfx/Models/CleanCommandOptions.cs b/src/docfx/Models/CleanCommandOptions.cs
new file mode 100644
index 00000000000..6b6817835db
--- /dev/null
+++ b/src/docfx/Models/CleanCommandOptions.cs
@@ -0,0 +1,21 @@
+// Licensed to the .NET Foundation under one or more agreements.
+// The .NET Foundation licenses this file to you under the MIT license.
+
+using System.ComponentModel;
+using Spectre.Console.Cli;
+
+#nullable enable
+
+namespace Docfx;
+
+[Description("Cleanup temporary files that are generated by docfx")]
+internal class CleanCommandOptions : LogOptions
+{
+    [Description("Path to docfx.json")]
+    [CommandArgument(0, "[config]")]
+    public required string ConfigFile { get; set; }
+
+    [Description("If set to true, skip file/directory delete operations")]
+    [CommandOption("--dryRun")]
+    public bool DryRun { get; set; }
+}
diff --git a/src/docfx/Program.cs b/src/docfx/Program.cs
index b71bb354f17..67780c1e90f 100644
--- a/src/docfx/Program.cs
+++ b/src/docfx/Program.cs
@@ -27,6 +27,7 @@ internal static int Main(string[] args)
             config.AddCommand<MetadataCommand>("metadata");
             config.AddCommand<ServeCommand>("serve");
             config.AddCommand<PdfCommand>("pdf");
+            config.AddCommand<CleanCommand>("clean");
             config.AddBranch("template", template =>
             {
                 template.AddCommand<TemplateCommand.ListCommand>("list");
diff --git a/src/docfx/Properties/launchSettings.json b/src/docfx/Properties/launchSettings.json
index 44553193297..9cb115be065 100644
--- a/src/docfx/Properties/launchSettings.json
+++ b/src/docfx/Properties/launchSettings.json
@@ -26,6 +26,14 @@
       "environmentVariables": {
       }
     },
+    // Run `docfx clean` command.
+    "docfx clean": {
+      "commandName": "Project",
+      "commandLineArgs": "clean ../../samples/seed/docfx.json",
+      "workingDirectory": ".",
+      "environmentVariables": {
+      }
+    },
     // Run `docfx serve` command and launch browser.
     "docfx serve": {
       "commandName": "Project",
diff --git a/test/docfx.Tests/CleanCommandTest.cs b/test/docfx.Tests/CleanCommandTest.cs
new file mode 100644
index 00000000000..b7ed731238d
--- /dev/null
+++ b/test/docfx.Tests/CleanCommandTest.cs
@@ -0,0 +1,126 @@
+// Licensed to the .NET Foundation under one or more agreements.
+// The .NET Foundation licenses this file to you under the MIT license.
+
+using AwesomeAssertions;
+using Docfx.Common;
+using Docfx.Tests.Common;
+
+#nullable enable
+
+namespace Docfx.Tests;
+
+[Collection("docfx STA")]
+public class CleanCommandTest : TestBase
+{
+    private readonly string projectFolder;
+
+    public CleanCommandTest()
+    {
+        projectFolder = GetRandomFolder();
+    }
+
+    [Fact]
+    public async Task TestCleanCommand()
+    {
+        // Arrange
+        var outputDir = Path.Combine(projectFolder, "_site");
+        var metadataDir = Path.Combine(projectFolder, "obj");
+        Directory.CreateDirectory(outputDir);
+        Directory.CreateDirectory(metadataDir);
+
+        File.Copy("Assets/docfx.sample.1.json", Path.Combine(projectFolder, "docfx.json"));
+        File.Copy("Assets/filter.yaml.sample", Path.Combine(outputDir, "sample.md"));
+        File.Copy("Assets/test.cs.sample.1", Path.Combine(metadataDir, "sample.yml"));
+
+        var context = new RunCleanContext
+        {
+            ConfigDirectory = projectFolder,
+            BuildOutputDirectory = outputDir,
+            MetadataOutputDirectories = [metadataDir],
+        };
+
+        // Act
+        RunClean.Exec(context);
+
+        // Assert
+        context.DeletedFilesCount.Should().Be(2);
+        context.SkippedFilesCount.Should().Be(0);
+
+        Directory.GetFileSystemEntries(outputDir).Should().BeEmpty();
+        Directory.GetFileSystemEntries(metadataDir).Should().BeEmpty();
+
+    }
+
+    [Fact]
+    public async Task TestCleanCommand_WithDryRun()
+    {
+        // Arrange
+        var outputDir = Path.Combine(projectFolder, "_site");
+        var metadataDir = Path.Combine(projectFolder, "obj");
+        Directory.CreateDirectory(outputDir);
+        Directory.CreateDirectory(metadataDir);
+
+        File.Copy("Assets/docfx.sample.1.json", Path.Combine(projectFolder, "docfx.json"));
+        File.Copy("Assets/filter.yaml.sample", Path.Combine(outputDir, "sample.md"));
+        File.Copy("Assets/test.cs.sample.1", Path.Combine(metadataDir, "sample.yml"));
+
+        var context = new RunCleanContext
+        {
+            ConfigDirectory = projectFolder,
+            BuildOutputDirectory = outputDir,
+            MetadataOutputDirectories = [metadataDir],
+            DryRun = true,
+        };
+
+        // Act
+        RunClean.Exec(context);
+
+        // Assert
+        context.DeletedFilesCount.Should().Be(0);
+        context.SkippedFilesCount.Should().Be(2);
+
+        Directory.GetFileSystemEntries(outputDir).Should().HaveCount(1);
+        Directory.GetFileSystemEntries(metadataDir).Should().HaveCount(1);
+    }
+
+    [Fact]
+    public async Task TestCleanCommand_WithExternalDirectory()
+    {
+        // Arrange
+        using var listener = new TestLoggerListener();
+        Logger.RegisterListener(listener);
+        try
+        {
+            var tempDir = GetRandomFolder();
+            var outputDir = Path.Combine(tempDir, "_site");
+            var metadataDir = Path.Combine(tempDir, "obj");
+            Directory.CreateDirectory(outputDir);
+            Directory.CreateDirectory(metadataDir);
+
+            File.Copy("Assets/docfx.sample.1.json", Path.Combine(projectFolder, "docfx.json"));
+            File.Copy("Assets/filter.yaml.sample", Path.Combine(outputDir, "sample.md"));
+            File.Copy("Assets/test.cs.sample.1", Path.Combine(metadataDir, "sample.yml"));
+
+            var context = new RunCleanContext
+            {
+                ConfigDirectory = projectFolder,
+                BuildOutputDirectory = outputDir,
+                MetadataOutputDirectories = [metadataDir],
+                DryRun = true,
+            };
+
+            // Act
+            RunClean.Exec(context);
+
+            // Assert
+            listener.Items.Where(x => x.LogLevel == LogLevel.Warning).Should().HaveCount(2);
+            context.DeletedFilesCount.Should().Be(0);
+            context.SkippedFilesCount.Should().Be(0);
+        }
+        finally
+        {
+            Logger.UnregisterListener(listener);
+            Logger.ResetCount();
+        }
+    }
+}
diff --git a/test/docfx.Tests/CommandLineTest.cs b/test/docfx.Tests/CommandLineTest.cs
index 66abb6b1288..e667ec4e62b 100644
--- a/test/docfx.Tests/CommandLineTest.cs
+++ b/test/docfx.Tests/CommandLineTest.cs
@@ -24,6 +24,7 @@ public static void PrintsHelp()
         Assert.Equal(0, Program.Main(["serve", "--help"]));
         Assert.Equal(0, Program.Main(["metadata", "--help"]));
         Assert.Equal(0, Program.Main(["pdf", "--help"]));
+        Assert.Equal(0, Program.Main(["clean", "--help"]));
         Assert.Equal(0, Program.Main(["init", "--help"]));
         Assert.Equal(0, Program.Main(["download", "--help"]));
         Assert.Equal(0, Program.Main(["merge", "--help"]));