diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index b088d7266..450f3939a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -1287,7 +1287,7 @@ private static void delete(File file, int depth, LockFile rLck)
 		File dir = file.getParentFile();
 		for (int i = 0; i < depth; ++i) {
 			try {
-				Files.delete(dir.toPath());
+				Files.deleteIfExists(dir.toPath());
 			} catch (DirectoryNotEmptyException e) {
 				// Don't log; normal case when there are other refs with the
 				// same prefix