diff --git a/python/packages/github_copilot/agent_framework_github_copilot/_agent.py b/python/packages/github_copilot/agent_framework_github_copilot/_agent.py
index 883810f9fc..0c72007083 100644
--- a/python/packages/github_copilot/agent_framework_github_copilot/_agent.py
+++ b/python/packages/github_copilot/agent_framework_github_copilot/_agent.py
@@ -196,6 +196,11 @@ class GitHubCopilotOptions(TypedDict, total=False):
     timeout: float
     """Request timeout in seconds. Defaults to GITHUB_COPILOT_TIMEOUT environment variable or 60 seconds."""
 
+    enable_file_hooks: bool
+    """Whether the session reads checkout-local ``.github/hooks/`` files. Defaults to
+    False so behavior does not depend on the working directory the agent runs in;
+    set True (via default_options or per-run options) to opt into checkout-driven hooks."""
+
     log_level: str
     """CLI log level. Defaults to GITHUB_COPILOT_LOG_LEVEL environment variable."""
 
@@ -1232,6 +1237,11 @@ def _build_session_kwargs(
         )
         kwargs["hooks"] = self._build_session_hooks(all_tools, kwargs)
 
+        # The SDK's default reads `.github/hooks/` from the process working
+        # directory, so identical agents would behave differently depending on
+        # where they were started. Pin it off unless the caller opts in.
+        kwargs.setdefault("enable_file_hooks", False)
+
         # Strip agent-internal and client-level keys that are consumed here or in the
         # run methods (and settings) but are NOT valid create_session parameters, so
         # they don't leak through the passthrough layer and raise TypeError.
diff --git a/python/packages/github_copilot/tests/test_github_copilot_agent.py b/python/packages/github_copilot/tests/test_github_copilot_agent.py
index 5e4ff52e05..a4241c65da 100644
--- a/python/packages/github_copilot/tests/test_github_copilot_agent.py
+++ b/python/packages/github_copilot/tests/test_github_copilot_agent.py
@@ -1125,6 +1125,7 @@ async def test_session_resumed_for_same_session(
             model=unittest.mock.ANY,
             on_permission_request=unittest.mock.ANY,
             hooks=unittest.mock.ANY,
+            enable_file_hooks=unittest.mock.ANY,
         )
 
     async def test_session_config_includes_model(
@@ -1904,6 +1905,35 @@ def runtime_hook(_input: Any, _context: Any) -> Any:
         # on_pre_tool_use is still honored via the hooks parameter.
         assert config["hooks"]["on_pre_tool_use"] is runtime_hook
 
+    async def test_enable_file_hooks_defaults_to_false(
+        self,
+        mock_client: MagicMock,
+    ) -> None:
+        """Sessions must not depend on the cwd: file hooks default to off."""
+        agent = GitHubCopilotAgent(client=mock_client)
+        await agent.start()
+
+        await agent._get_or_create_session(AgentSession())  # type: ignore[reportPrivateUsage]
+
+        config = mock_client.create_session.call_args.kwargs
+        assert config["enable_file_hooks"] is False
+
+    async def test_enable_file_hooks_opt_in_wins(
+        self,
+        mock_client: MagicMock,
+    ) -> None:
+        """A caller who wants checkout-driven hooks can turn them back on."""
+        agent = GitHubCopilotAgent(
+            client=mock_client,
+            default_options=cast(Any, {"enable_file_hooks": True}),
+        )
+        await agent.start()
+
+        await agent._get_or_create_session(AgentSession())  # type: ignore[reportPrivateUsage]
+
+        config = mock_client.create_session.call_args.kwargs
+        assert config["enable_file_hooks"] is True
+
 
 class TestGitHubCopilotAgentToolConversion:
     """Test cases for tool conversion."""
@@ -3667,3 +3697,4 @@ async def test_integration_run_with_shell_permissions_executes_command() -> None
 
         if isinstance(session.service_session_id, str) and agent._client:
             await agent._client.delete_session(session.service_session_id)
+