diff --git a/codemcp/__init__.py b/codemcp/__init__.py
index 956dde18..a9ee2048 100644
--- a/codemcp/__init__.py
+++ b/codemcp/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 from .hot_reload_entry import run as run_hot_reload
-from .main import codemcp, configure_logging, mcp, run
+from .main import cli, codemcp, configure_logging, mcp, run
 from .shell import get_subprocess_env, run_command
 
 __all__ = [
@@ -12,4 +12,5 @@
     "codemcp",
     "run_command",
     "get_subprocess_env",
+    "cli",
 ]
diff --git a/codemcp/__main__.py b/codemcp/__main__.py
index 4f775249..346061fb 100644
--- a/codemcp/__main__.py
+++ b/codemcp/__main__.py
@@ -2,9 +2,10 @@
 
 # WARNING: do NOT do a relative import, this file must be directly executable
 # by filename
-from codemcp import mcp, run
+from codemcp import cli, mcp
 
 __all__ = ["mcp"]
 
 if __name__ == "__main__":
-    run()
+    # Use Click's CLI interface instead of directly calling run()
+    cli()
diff --git a/codemcp/main.py b/codemcp/main.py
index 5dc15cc7..54677917 100644
--- a/codemcp/main.py
+++ b/codemcp/main.py
@@ -2,7 +2,11 @@
 
 import logging
 import os
+import sys
+from pathlib import Path
+from typing import Optional
 
+import click
 from mcp.server.fastmcp import FastMCP
 
 from .tools.chmod import chmod
@@ -406,6 +410,91 @@ def filter(self, record):
         logging.info("Logs from 'mcp' module are being filtered")
 
 
+def init_codemcp_project(path: str) -> str:
+    """Initialize a new codemcp project.
+
+    Args:
+        path: Path to initialize the project in
+
+    Returns:
+        Message indicating success or failure
+    """
+    import subprocess
+
+    try:
+        # Convert to Path object and resolve to absolute path
+        project_path = Path(path).resolve()
+
+        # Create directory if it doesn't exist
+        project_path.mkdir(parents=True, exist_ok=True)
+
+        # Check if git repository already exists
+        git_dir = project_path / ".git"
+        if not git_dir.exists():
+            # Initialize git repository
+            subprocess.run(["git", "init"], cwd=project_path, check=True)
+            print(f"Initialized git repository in {project_path}")
+        else:
+            print(f"Git repository already exists in {project_path}")
+
+        # Create empty codemcp.toml file if it doesn't exist
+        config_file = project_path / "codemcp.toml"
+        if not config_file.exists():
+            with open(config_file, "w") as f:
+                f.write("# codemcp configuration file\n\n")
+            print(f"Created empty codemcp.toml file in {project_path}")
+        else:
+            print(f"codemcp.toml file already exists in {project_path}")
+
+        # Make initial commit if there are no commits yet
+        try:
+            # Check if there are any commits
+            result = subprocess.run(
+                ["git", "rev-parse", "HEAD"],
+                cwd=project_path,
+                check=False,
+                capture_output=True,
+                text=True,
+            )
+
+            if result.returncode != 0:
+                # No commits yet, add codemcp.toml and make initial commit
+                subprocess.run(
+                    ["git", "add", "codemcp.toml"], cwd=project_path, check=True
+                )
+                subprocess.run(
+                    ["git", "commit", "-m", "chore: initialize codemcp project"],
+                    cwd=project_path,
+                    check=True,
+                )
+                print("Created initial commit with codemcp.toml")
+            else:
+                print("Repository already has commits, not creating initial commit")
+        except subprocess.CalledProcessError as e:
+            print(f"Warning: Failed to create initial commit: {e}")
+
+        return f"Successfully initialized codemcp project in {project_path}"
+    except Exception as e:
+        return f"Error initializing project: {e}"
+
+
+@click.group(invoke_without_command=True)
+@click.pass_context
+def cli(ctx):
+    """CodeMCP: Command-line interface for MCP server and project management."""
+    # If no subcommand is provided, run the MCP server (for backwards compatibility)
+    if ctx.invoked_subcommand is None:
+        run()
+
+
+@cli.command()
+@click.argument("path", type=click.Path(), default=".")
+def init(path):
+    """Initialize a new codemcp project with an empty codemcp.toml file and git repository."""
+    result = init_codemcp_project(path)
+    click.echo(result)
+
+
 def run():
     """Run the MCP server."""
     configure_logging()
diff --git a/e2e/test_init_command.py b/e2e/test_init_command.py
new file mode 100644
index 00000000..80b70371
--- /dev/null
+++ b/e2e/test_init_command.py
@@ -0,0 +1,71 @@
+#!/usr/bin/env python3
+
+import subprocess
+import tempfile
+from pathlib import Path
+
+from codemcp.main import init_codemcp_project
+
+
+def test_init_command():
+    """Test the init command creates a codemcp.toml file and initializes a git repo."""
+    # Create a temporary directory for testing
+    with tempfile.TemporaryDirectory() as temp_dir:
+        # Run the init_codemcp_project function
+        result = init_codemcp_project(temp_dir)
+
+        # Check that the function reports success
+        assert "Successfully initialized" in result
+
+        # Check that codemcp.toml was created
+        config_file = Path(temp_dir) / "codemcp.toml"
+        assert config_file.exists()
+
+        # Check that git repository was initialized
+        git_dir = Path(temp_dir) / ".git"
+        assert git_dir.is_dir()
+
+        # Check that a commit was created
+        result = subprocess.run(
+            ["git", "log", "--oneline"],
+            cwd=temp_dir,
+            capture_output=True,
+            text=True,
+            check=True,
+        )
+        assert "initialize codemcp project" in result.stdout
+
+
+def test_init_command_existing_repo():
+    """Test the init command works with an existing git repository."""
+    # Create a temporary directory for testing
+    with tempfile.TemporaryDirectory() as temp_dir:
+        # Initialize git repository first
+        subprocess.run(["git", "init"], cwd=temp_dir, check=True)
+
+        # Make a dummy commit to simulate existing repository
+        dummy_file = Path(temp_dir) / "dummy.txt"
+        dummy_file.write_text("test content")
+
+        subprocess.run(
+            ["git", "config", "user.name", "Test User"], cwd=temp_dir, check=True
+        )
+        subprocess.run(
+            ["git", "config", "user.email", "test@example.com"],
+            cwd=temp_dir,
+            check=True,
+        )
+        subprocess.run(["git", "add", "dummy.txt"], cwd=temp_dir, check=True)
+        subprocess.run(
+            ["git", "commit", "-m", "Initial commit"], cwd=temp_dir, check=True
+        )
+
+        # Run the init_codemcp_project function
+        result = init_codemcp_project(temp_dir)
+
+        # Check that the function reports success
+        assert "Successfully initialized" in result
+
+        # Check that codemcp.toml was created
+        config_file = Path(temp_dir) / "codemcp.toml"
+        assert config_file.exists()
diff --git a/pyproject.toml b/pyproject.toml
index 538419d8..7c90a130 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,6 +14,7 @@ dependencies = [
     "pyyaml>=6.0.0",
     "pytest-xdist>=3.6.1",
     "editorconfig>=0.17.0",
+    "click>=8.1.8",
 ]
 
 [dependency-groups]
@@ -28,7 +29,7 @@ dev = [
 ]
 
 [project.scripts]
-codemcp = "codemcp:run"
+codemcp = "codemcp:cli"
 codemcp-multi = "codemcp.multi_entry:main"
 
 [build-system]
diff --git a/uv.lock b/uv.lock
index 7bdcc81b..4affd1d9 100644
--- a/uv.lock
+++ b/uv.lock
@@ -76,6 +76,7 @@ version = "0.5.0"
 source = { editable = "." }
 dependencies = [
     { name = "anyio" },
+    { name = "click" },
     { name = "editorconfig" },
     { name = "mcp", extra = ["cli"] },
     { name = "pytest-xdist" },
@@ -99,6 +100,7 @@ dev = [
 [package.metadata]
 requires-dist = [
     { name = "anyio", specifier = ">=3.7.0" },
+    { name = "click", specifier = ">=8.1.8" },
     { name = "editorconfig", specifier = ">=0.17.0" },
     { name = "mcp", extras = ["cli"], specifier = ">=1.2.0" },
     { name = "pytest-xdist", specifier = ">=3.6.1" },