diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackCompactor.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackCompactor.java
index ea563926b..83728842b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackCompactor.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackCompactor.java
@@ -220,8 +220,14 @@ public void compact(ProgressMonitor pm) throws IOException {
 				pw.setReuseDeltaCommits(false);
 
 				addObjectsToPack(pw, ctx, pm);
-				if (pw.getObjectCount() == 0)
+				if (pw.getObjectCount() == 0) {
+					List<DfsPackDescription> remove = toPrune();
+					if (remove.size() > 0)
+						objdb.commitPack(
+								Collections.<DfsPackDescription>emptyList(),
+								remove);
 					return;
+				}
 
 				boolean rollback = true;
 				DfsPackDescription pack = objdb.newPack(COMPACT);