diff --git a/fast-import.c b/fast-import.c
index 613623be14..7563e43a39 100644
--- a/fast-import.c
+++ b/fast-import.c
@@ -2166,6 +2166,12 @@ static void file_change_m(struct branch *b)
 		p = uq.buf;
 	}
 
+	/* Git does not track empty, non-toplevel directories. */
+	if (S_ISDIR(mode) && !memcmp(sha1, EMPTY_TREE_SHA1_BIN, 20) && *p) {
+		tree_content_remove(&b->branch_tree, p, NULL);
+		return;
+	}
+
 	if (S_ISGITLINK(mode)) {
 		if (inline_data)
 			die("Git links cannot be specified 'inline': %s",
diff --git a/t/t9300-fast-import.sh b/t/t9300-fast-import.sh
index 7c059204e9..385e78c22c 100755
--- a/t/t9300-fast-import.sh
+++ b/t/t9300-fast-import.sh
@@ -874,6 +874,48 @@ test_expect_success \
 	 git diff-tree -C --find-copies-harder -r N4^ N4 >actual &&
 	 compare_diff_raw expect actual'
 
+test_expect_success \
+	'N: delete directory by copying' \
+	'cat >expect <<-\EOF &&
+	OBJID
+	:100644 000000 OBJID OBJID D	foo/bar/qux
+	OBJID
+	:000000 100644 OBJID OBJID A	foo/bar/baz
+	:000000 100644 OBJID OBJID A	foo/bar/qux
+	EOF
+	 empty_tree=$(git mktree </dev/null) &&
+	 cat >input <<-INPUT_END &&
+	commit refs/heads/N-delete
+	committer $GIT_COMMITTER_NAME <$GIT_COMMITTER_EMAIL> $GIT_COMMITTER_DATE
+	data <<COMMIT
+	collect data to be deleted
+	COMMIT
+
+	deleteall
+	M 100644 inline foo/bar/baz
+	data <<DATA_END
+	hello
+	DATA_END
+	C "foo/bar/baz" "foo/bar/qux"
+	C "foo/bar/baz" "foo/bar/quux/1"
+	C "foo/bar/baz" "foo/bar/quuux"
+	M 040000 $empty_tree foo/bar/quux
+	M 040000 $empty_tree foo/bar/quuux
+
+	commit refs/heads/N-delete
+	committer $GIT_COMMITTER_NAME <$GIT_COMMITTER_EMAIL> $GIT_COMMITTER_DATE
+	data <<COMMIT
+	delete subdirectory
+	COMMIT
+
+	M 040000 $empty_tree foo/bar/qux
+	INPUT_END
+	 git fast-import <input &&
+	 git rev-list N-delete |
+		git diff-tree -r --stdin --root --always |
+		sed -e "s/$_x40/OBJID/g" >actual &&
+	 test_cmp expect actual'
+
 test_expect_success \
 	'N: modify copied tree' \
 	'cat >expect <<-\EOF &&