diff --git a/dvc/state.py b/dvc/state.py
index 3c978355b..15a4b0678 100644
--- a/dvc/state.py
+++ b/dvc/state.py
@@ -449,6 +449,7 @@ class State(StateBase):  # pylint: disable=too-many-instance-attributes
                 remove(path)
                 unused.append(relpath)
 
-        for relpath in unused:
-            cmd = "DELETE FROM {} WHERE path = ?".format(self.LINK_STATE_TABLE)
-            self._execute(cmd, (relpath,))
+        cmd = "DELETE FROM {} WHERE path IN ({})".format(
+            self.LINK_STATE_TABLE, ",".join(["?"] * len(unused))
+        )
+        self._execute(cmd, tuple(unused))
diff --git a/tests/func/test_state.py b/tests/func/test_state.py
index edc2012bf..e3d914eeb 100644
--- a/tests/func/test_state.py
+++ b/tests/func/test_state.py
@@ -77,3 +77,21 @@ class TestGetStateRecordForInode(TestDvc):
             state.save(PathInfo(path), md5)
             ret = state.get_state_record_for_inode(inode)
             self.assertIsNotNone(ret)
+
+
+def test_remove_unused_links(repo_dir, dvc_repo):
+    stages = dvc_repo.add(repo_dir.FOO)
+    assert len(stages) == 1
+
+    stages = dvc_repo.add(repo_dir.BAR)
+    assert len(stages) == 1
+
+    cmd_count_links = "SELECT count(*) FROM {}".format(State.LINK_STATE_TABLE)
+    with dvc_repo.state:
+        result = dvc_repo.state._execute(cmd_count_links).fetchone()[0]
+        assert result == 2
+
+        dvc_repo.state.remove_unused_links([])
+
+        result = dvc_repo.state._execute(cmd_count_links).fetchone()[0]
+        assert result == 0