diff --git a/.chronus/changes/python-fix-customized-namespace-2025-6-23-2-6-58.md b/.chronus/changes/python-fix-customized-namespace-2025-6-23-2-6-58.md
new file mode 100644
index 00000000000..09a243cadca
--- /dev/null
+++ b/.chronus/changes/python-fix-customized-namespace-2025-6-23-2-6-58.md
@@ -0,0 +1,7 @@
+---
+changeKind: fix
+packages:
+  - "@typespec/http-client-python"
+---
+
+Don't overwrite existing pkgutil init file
\ No newline at end of file
diff --git a/packages/http-client-python/generator/pygen/codegen/serializers/__init__.py b/packages/http-client-python/generator/pygen/codegen/serializers/__init__.py
index d3a3766479a..4c8f68b520c 100644
--- a/packages/http-client-python/generator/pygen/codegen/serializers/__init__.py
+++ b/packages/http-client-python/generator/pygen/codegen/serializers/__init__.py
@@ -154,11 +154,13 @@ def serialize(self) -> None:
                 # add clients folder if there are clients in this namespace
                 self._serialize_client_and_config_files(client_namespace, client_namespace_type.clients, env)
             else:
-                # add pkgutil init file if no clients in this namespace
-                self.write_file(
-                    exec_path / Path("__init__.py"),
-                    general_serializer.serialize_pkgutil_init_file(),
+                # add/keep pkgutil init file if no clients in this namespace
+                init_path = exec_path / Path("__init__.py")
+                original_init_content = self.read_file(init_path)
+                init_content = (
+                    original_init_content if original_init_content else general_serializer.serialize_pkgutil_init_file()
                 )
+                self.write_file(init_path, init_content)
 
             # _utils/py.typed/_types.py/_validation.py
             # is always put in top level namespace