diff --git a/apps/api/app/api/routes/chunked_upload.py b/apps/api/app/api/routes/chunked_upload.py
index ff9a2c8d2..45664d786 100644
--- a/apps/api/app/api/routes/chunked_upload.py
+++ b/apps/api/app/api/routes/chunked_upload.py
@@ -3,6 +3,7 @@ Chunked upload routes for large file uploads (up to 2GB).
 Supports chunked upload, resume, and automatic cleanup of expired uploads.
 """
 
+import fcntl
 import json
 import logging
 import os
@@ -64,6 +65,33 @@ def _get_upload_meta_path(upload_id: str) -> Path:
     return CHUNK_STORAGE_ROOT / f"{upload_id}.meta.json"
 
 
+def _atomic_check_and_record(upload_id: str, chunk_index: int) -> bool:
+    """
+    Atomically check if chunk is uploaded and record if not.
+    Uses file locking to prevent race conditions.
+    
+    Returns:
+        True if chunk was newly recorded, False if already exists
+    """
+    meta_path = _get_upload_meta_path(upload_id)
+    CHUNK_STORAGE_ROOT.mkdir(parents=True, exist_ok=True)
+    
+    with open(meta_path, "r+", encoding="utf-8") as f:
+        fcntl.flock(f.fileno(), fcntl.LOCK_EX)
+        try:
+            meta = json.load(f)
+            if chunk_index in meta["uploaded_chunks"]:
+                return False
+            meta["uploaded_chunks"].append(chunk_index)
+            meta["status"] = "uploading"
+            f.seek(0)
+            json.dump(meta, f, ensure_ascii=False, indent=2)
+            f.truncate()
+            return True
+        finally:
+            fcntl.flock(f.fileno(), fcntl.LOCK_UN)
+
+
 def _require_workspace_member(
     workspace_id: str,
     authenticated_user: AuthenticatedUser,
@@ -144,7 +172,8 @@ def _cleanup_expired_uploads() -> int:
             if expires_at.tzinfo is None:
                 expires_at = expires_at.replace(tzinfo=timezone.utc)
 
-            if expires_at < now:
+            # Only cleanup uploads that are not actively being uploaded
+    if expires_at < now and meta.get("status") != "uploading":
                 upload_id = meta["upload_id"]
                 chunk_dir = _get_chunk_dir(upload_id)
                 if chunk_dir.exists():
@@ -270,8 +299,8 @@ async def upload_chunk(
     # Verify permission
     _require_workspace_member(meta["workspace_id"], authenticated_user, workspace_member_repository)
 
-    # Check if already uploaded
-    if chunk_index in meta["uploaded_chunks"]:
+    # Atomic check and record to prevent race conditions
+    if not _atomic_check_and_record(upload_id, chunk_index):
         return {"message": "Chunk already uploaded", "chunk_index": chunk_index}
 
     # Read chunk data
@@ -283,6 +312,19 @@ async def upload_chunk(
         expected_size = meta["file_size"] - (chunk_index * DEFAULT_CHUNK_SIZE)
 
     if len(chunk_data) != expected_size:
+        # Rollback the recorded chunk
+        meta_path = _get_upload_meta_path(upload_id)
+        with open(meta_path, "r+", encoding="utf-8") as f:
+            fcntl.flock(f.fileno(), fcntl.LOCK_EX)
+            try:
+                meta = json.load(f)
+                if chunk_index in meta["uploaded_chunks"]:
+                    meta["uploaded_chunks"].remove(chunk_index)
+                f.seek(0)
+                json.dump(meta, f, ensure_ascii=False, indent=2)
+                f.truncate()
+            finally:
+                fcntl.flock(f.fileno(), fcntl.LOCK_UN)
         raise HTTPException(
             status_code=status.HTTP_400_BAD_REQUEST,
             detail=f"Chunk size mismatch. Expected {expected_size}, got {len(chunk_data)}",
@@ -293,10 +335,8 @@ async def upload_chunk(
     with open(chunk_path, "wb") as f:
         f.write(chunk_data)
 
-    # Update metadata
-    meta["uploaded_chunks"].append(chunk_index)
-    meta["status"] = "uploading"
-    _save_upload_meta(upload_id, meta)
+    # Reload metadata for response
+    meta = _load_upload_meta(upload_id)
 
     return {
         "message": "Chunk uploaded successfully",