diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/CleanFilter.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/CleanFilter.java
index 66feca751..c4e34eed0 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/CleanFilter.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/CleanFilter.java
@@ -151,7 +151,10 @@ public int run() throws IOException {
 						FileUtils.delete(tmpFile.toFile());
 					}
 				} else {
-					FileUtils.mkdirs(mediaFile.getParent().toFile(), true);
+					Path parent = mediaFile.getParent();
+					if (parent != null) {
+						FileUtils.mkdirs(parent.toFile(), true);
+					}
 					FileUtils.rename(tmpFile.toFile(), mediaFile.toFile(),
 							StandardCopyOption.ATOMIC_MOVE);
 				}