diff --git a/transfer_service/file_cleaner.py b/transfer_service/file_cleaner.py
index 73d842d95d043f367bbfdb3273954372b9eea0ba..533c4343a58b689d0c32064ca3b0d7c46f1bfc5e 100644
--- a/transfer_service/file_cleaner.py
+++ b/transfer_service/file_cleaner.py
@@ -74,14 +74,15 @@ class FileCleaner(object):
                 nodeId = row["node_id"]
                 delta = cTime - dTime
                 if delta.days >= self.days and delta.seconds > self.seconds:
-                    os.remove(filePath)
-                    self.logger.debug(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S") + ' ' + filePath)
+                    if os.path.exists(filePath):
+                        os.remove(filePath)
+                        self.logger.debug(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S") + ' ' + filePath)
                     try:
                         self.dbConn.setPhyDeletedOn(nodeId)
                     except Exception:
                         self.logger.exception(f"FATAL: unable to set the 'phy_deleted_on' flag for VOSpace node having ID = {nodeId}")
                         return
-                    if basePath not in basePaths:
+                    if os.path.exists(basePath) and basePath not in basePaths:
                         basePaths.append(basePath)
             self.logger.info("Removing empty folders (if any)...")
             for basePath in basePaths: