diff --git a/src/integrations/prefect-github/prefect_github/repository.py b/src/integrations/prefect-github/prefect_github/repository.py
index da2d7581cd95..4742bc2d8117 100644
--- a/src/integrations/prefect-github/prefect_github/repository.py
+++ b/src/integrations/prefect-github/prefect_github/repository.py
@@ -121,7 +121,8 @@ async def get_directory(
         # Clone to a temporary directory and move the subdirectory over
         with TemporaryDirectory(suffix="prefect") as tmp_dir:
             tmp_path_str = tmp_dir
-            cmd += f" {tmp_path_str}"
+            # wrap the directory with quotes, because shlex removes windows-style slashes "//" - fixes issue 13180
+            cmd += f' "{tmp_path_str}"'
             cmd = shlex.split(cmd)
 
             err_stream = io.StringIO()