diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
index 48ea13b98..ea8dfa293 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
@@ -45,11 +45,14 @@ package org.eclipse.jgit.internal.storage.file;
 
 import static java.lang.Integer.valueOf;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.concurrent.BrokenBarrierException;
 import java.util.concurrent.Callable;
 import java.util.concurrent.CyclicBarrier;
@@ -80,6 +83,17 @@ public class GcPackRefsTest extends GcTestCase {
 		assertSame(repo.exactRef("refs/tags/t").getStorage(), Storage.PACKED);
 	}
 
+	@Test
+	public void emptyRefDirectoryDeleted() throws Exception {
+		String ref = "dir/ref";
+		tr.branch(ref).commit().create();
+		String name = repo.findRef(ref).getName();
+		Path dir = repo.getDirectory().toPath().resolve(name).getParent();
+
+		gc.packRefs();
+		assertFalse(Files.exists(dir));
+	}
+
 	@Test
 	public void concurrentOnlyOneWritesPackedRefs() throws Exception {
 		RevBlob a = tr.blob("a");
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 4bb2982b4..e5ca73682 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
@@ -688,7 +688,7 @@ public class RefDirectory extends RefDatabase {
 							newLoose = curLoose.remove(idx);
 						} while (!looseRefs.compareAndSet(curLoose, newLoose));
 						int levels = levelsIn(refName) - 2;
-						delete(fileFor(refName), levels);
+						delete(refFile, levels, rLck);
 					}
 				} finally {
 					rLck.unlock();
@@ -1062,13 +1062,24 @@ public class RefDirectory extends RefDatabase {
 	}
 
 	static void delete(final File file, final int depth) throws IOException {
-		if (!file.delete() && file.isFile())
-			throw new IOException(MessageFormat.format(JGitText.get().fileCannotBeDeleted, file));
+		delete(file, depth, null);
+	}
 
+	private static void delete(final File file, final int depth, LockFile rLck)
+			throws IOException {
+		if (!file.delete() && file.isFile()) {
+			throw new IOException(MessageFormat.format(
+					JGitText.get().fileCannotBeDeleted, file));
+		}
+
+		if (rLck != null) {
+			rLck.unlock(); // otherwise cannot delete dir below
+		}
 		File dir = file.getParentFile();
 		for (int i = 0; i < depth; ++i) {
-			if (!dir.delete())
+			if (!dir.delete()) {
 				break; // ignore problem here
+			}
 			dir = dir.getParentFile();
 		}
 	}