diff --git a/edkrepo/commands/sync_command.py b/edkrepo/commands/sync_command.py
index 32c1df7..d9b4664 100644
--- a/edkrepo/commands/sync_command.py
+++ b/edkrepo/commands/sync_command.py
@@ -514,7 +514,7 @@ def __check_submodule_config(self, workspace_path, manifest, repo_sources):
         try:
             local_manifest_dir = os.path.join(workspace_path, "repo")
             prefix_required = find_git_version() >= GitVersion('2.34.0')
-            includeif_regex = re.compile('^includeIf "gitdir:{}(/.+)/"$'.format('%\(prefix\)' if prefix_required else ''))
+            includeif_regex = re.compile('^includeIf "gitdir:{}(/.+)/"$'.format('%\\(prefix\\)' if prefix_required else ''))
             rewrite_everything = False
             #Generate list of .gitconfig files that should be present in the workspace
             included_configs = []
diff --git a/edkrepo/common/workspace_maintenance/git_config_maintenance.py b/edkrepo/common/workspace_maintenance/git_config_maintenance.py
index b993e38..cee3414 100644
--- a/edkrepo/common/workspace_maintenance/git_config_maintenance.py
+++ b/edkrepo/common/workspace_maintenance/git_config_maintenance.py
@@ -22,10 +22,10 @@ def clean_git_globalconfig():
     prefix_required = find_git_version() >= GitVersion('2.34.0')
     with git.GitConfigParser(global_gitconfig_path, read_only=False) as git_globalconfig:
         if prefix_required:
-            includeif_regex = re.compile('^includeIf "gitdir:%\(prefix\)(/.+)/"$')
+            includeif_regex = re.compile('^includeIf "gitdir:%\\(prefix\\)(/.+)/"$')
             includeif_regex_old = re.compile('^includeIf "gitdir:(/.+)/"$')
         else:
-            includeif_regex_old = re.compile('^includeIf "gitdir:%\(prefix\)(/.+)/"$')
+            includeif_regex_old = re.compile('^includeIf "gitdir:%\\(prefix\\)(/.+)/"$')
             includeif_regex = re.compile('^includeIf "gitdir:(/.+)/"$')
         for section in git_globalconfig.sections():
             data = includeif_regex.match(section)