diff --git a/src/cli/cli.ts b/src/cli/cli.ts
index 817b659..5ba121c 100644
--- a/src/cli/cli.ts
+++ b/src/cli/cli.ts
@@ -101,22 +101,33 @@ program
 program
   .command("pack [directory] [output]")
   .description("Pack a directory into an MCPB extension")
-  .action((directory: string = process.cwd(), output?: string) => {
-    void (async () => {
-      try {
-        const success = await packExtension({
-          extensionPath: directory,
-          outputPath: output,
-        });
-        process.exit(success ? 0 : 1);
-      } catch (error) {
-        console.error(
-          `ERROR: ${error instanceof Error ? error.message : "Unknown error"}`,
-        );
-        process.exit(1);
-      }
-    })();
-  });
+  .option(
+    "-m, --manifest <path>",
+    "Path to manifest file (defaults to manifest.json in directory)",
+  )
+  .action(
+    (
+      directory: string = process.cwd(),
+      output: string | undefined,
+      options: { manifest?: string },
+    ) => {
+      void (async () => {
+        try {
+          const success = await packExtension({
+            extensionPath: directory,
+            outputPath: output,
+            manifestPath: options.manifest,
+          });
+          process.exit(success ? 0 : 1);
+        } catch (error) {
+          console.error(
+            `ERROR: ${error instanceof Error ? error.message : "Unknown error"}`,
+          );
+          process.exit(1);
+        }
+      })();
+    },
+  );
 
 // Unpack command
 program
diff --git a/src/cli/pack.ts b/src/cli/pack.ts
index e2411bf..1e35d47 100644
--- a/src/cli/pack.ts
+++ b/src/cli/pack.ts
@@ -22,6 +22,7 @@ interface PackOptions {
   extensionPath: string;
   outputPath?: string;
   silent?: boolean;
+  manifestPath?: string;
 }
 
 function formatFileSize(bytes: number): string {
@@ -50,6 +51,7 @@ export async function packExtension({
   extensionPath,
   outputPath,
   silent,
+  manifestPath: customManifestPath,
 }: PackOptions): Promise<boolean> {
   const resolvedPath = resolve(extensionPath);
   const logger = getLogger({ silent });
@@ -60,9 +62,18 @@ export async function packExtension({
     return false;
   }
 
-  // Check if manifest exists
-  const manifestPath = join(resolvedPath, "manifest.json");
+  // Resolve manifest path
+  const manifestPath = customManifestPath
+    ? resolve(customManifestPath)
+    : join(resolvedPath, "manifest.json");
+
   if (!existsSync(manifestPath)) {
+    if (customManifestPath) {
+      // When --manifest is explicitly provided, error immediately
+      logger.error(`ERROR: Manifest file not found: ${customManifestPath}`);
+      return false;
+    }
+
     logger.log(`No manifest.json found in ${extensionPath}`);
     const shouldInit = await confirm({
       message: "Would you like to create a manifest.json file?",
@@ -135,6 +146,15 @@ export async function packExtension({
       mcpbIgnorePatterns,
     );
 
+    // When using a custom manifest path, inject the manifest into the bundle
+    if (customManifestPath) {
+      const manifestStat = statSync(manifestPath);
+      files["manifest.json"] = {
+        data: readFileSync(manifestPath),
+        mode: manifestStat.mode,
+      };
+    }
+
     // Print package header
     logger.log(`\n📦  ${manifest.name}@${manifest.version}`);
 
diff --git a/test/cli.test.ts b/test/cli.test.ts
index e7757ac..2586d7c 100644
--- a/test/cli.test.ts
+++ b/test/cli.test.ts
@@ -258,6 +258,84 @@ describe("DXT CLI", () => {
       expect(originalFile2).toEqual(unpackedFile2);
     });
 
+    it("should pack with --manifest pointing to a separate directory", () => {
+      const projectDir = join(__dirname, "temp-manifest-project");
+      const manifestDir = join(__dirname, "temp-manifest-separate");
+      const manifestPackedPath = join(__dirname, "test-manifest-flag.mcpb");
+
+      try {
+        // Create project directory with source files (no manifest)
+        fs.mkdirSync(join(projectDir, "server"), { recursive: true });
+        fs.writeFileSync(
+          join(projectDir, "server", "index.js"),
+          "console.log('hello');",
+        );
+
+        // Create separate manifest directory
+        fs.mkdirSync(manifestDir, { recursive: true });
+        fs.writeFileSync(
+          join(manifestDir, "manifest.json"),
+          JSON.stringify({
+            manifest_version: DEFAULT_MANIFEST_VERSION,
+            name: "Test Separate Manifest",
+            version: "1.0.0",
+            description: "Test with separate manifest",
+            author: { name: "MCPB" },
+            server: {
+              type: "node",
+              entry_point: "server/index.js",
+              mcp_config: { command: "node" },
+            },
+          }),
+        );
+
+        const result = execSync(
+          `node ${cliPath} pack ${projectDir} ${manifestPackedPath} --manifest ${join(manifestDir, "manifest.json")}`,
+          { encoding: "utf-8" },
+        );
+
+        expect(fs.existsSync(manifestPackedPath)).toBe(true);
+        expect(result).toContain("Validating manifest");
+      } finally {
+        fs.rmSync(projectDir, { recursive: true, force: true });
+        fs.rmSync(manifestDir, { recursive: true, force: true });
+        if (fs.existsSync(manifestPackedPath)) {
+          fs.unlinkSync(manifestPackedPath);
+        }
+      }
+    });
+
+    it("should fail with --manifest pointing to nonexistent file", () => {
+      const projectDir = join(__dirname, "temp-manifest-missing-project");
+
+      try {
+        fs.mkdirSync(projectDir, { recursive: true });
+        fs.writeFileSync(join(projectDir, "index.js"), "console.log('hello');");
+
+        expect(() => {
+          execSync(
+            `node ${cliPath} pack ${projectDir} /tmp/out.mcpb --manifest /nonexistent/manifest.json`,
+            { encoding: "utf-8", stdio: "pipe" },
+          );
+        }).toThrow();
+
+        try {
+          execSync(
+            `node ${cliPath} pack ${projectDir} /tmp/out.mcpb --manifest /nonexistent/manifest.json`,
+            { encoding: "utf-8", stdio: "pipe" },
+          );
+        } catch (error: unknown) {
+          const execError = error as { stdout?: Buffer; stderr?: Buffer };
+          const output =
+            (execError.stdout?.toString() || "") +
+            (execError.stderr?.toString() || "");
+          expect(output).toContain("Manifest file not found");
+        }
+      } finally {
+        fs.rmSync(projectDir, { recursive: true, force: true });
+      }
+    });
+
     it("should preserve executable file permissions after packing and unpacking", () => {
       // Skip this test on Windows since it doesn't support Unix permissions
       if (process.platform === "win32") {