diff --git a/backend/windmill-api/src/workspaces.rs b/backend/windmill-api/src/workspaces.rs
index e6f59413c4..6c61ff9ae8 100644
--- a/backend/windmill-api/src/workspaces.rs
+++ b/backend/windmill-api/src/workspaces.rs
@@ -1154,8 +1154,10 @@ async fn delete_git_sync_repository(
 ) -> Result<String> {
     require_admin(is_admin, &username)?;
 
-    // Validate the resource path format
-    validate_git_repo_resource_path(&request.git_repo_resource_path)?;
+    // For deletion, only validate that path is not empty to allow cleanup of malformed entries
+    if request.git_repo_resource_path.is_empty() {
+        return Err(Error::BadRequest("Resource path cannot be empty".to_string()));
+    }
 
     let mut tx = db.begin().await?;
 
diff --git a/frontend/src/lib/components/git_sync/GitSyncContext.svelte.ts b/frontend/src/lib/components/git_sync/GitSyncContext.svelte.ts
index 16b313b0e6..121bbad81b 100644
--- a/frontend/src/lib/components/git_sync/GitSyncContext.svelte.ts
+++ b/frontend/src/lib/components/git_sync/GitSyncContext.svelte.ts
@@ -192,7 +192,7 @@ export function createGitSyncContext(workspace: string) {
 		)
 
 		// Only call backend API if repository exists in the saved state
-		if (existsInInitialState && repo.git_repo_resource_path) {
+		if (existsInInitialState) {
 			await WorkspaceService.deleteGitSyncRepository({
 				workspace,
 				requestBody: {