diff --git a/changelogs/unreleased/sh-remove-orphaned-label-links.yml b/changelogs/unreleased/sh-remove-orphaned-label-links.yml
new file mode 100644
index 00000000000..b035b57ff1b
--- /dev/null
+++ b/changelogs/unreleased/sh-remove-orphaned-label-links.yml
@@ -0,0 +1,5 @@
+---
+title: Remove orphaned label links
+merge_request: 21552
+author:
+type: fixed
diff --git a/db/post_migrate/20180906051323_remove_orphaned_label_links.rb b/db/post_migrate/20180906051323_remove_orphaned_label_links.rb
new file mode 100644
index 00000000000..b56b74f483e
--- /dev/null
+++ b/db/post_migrate/20180906051323_remove_orphaned_label_links.rb
@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+class RemoveOrphanedLabelLinks < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+
+  disable_ddl_transaction!
+
+  class LabelLinks < ActiveRecord::Base
+    self.table_name = 'label_links'
+    include EachBatch
+
+    def self.orphaned
+      where('NOT EXISTS ( SELECT 1 FROM labels WHERE labels.id = label_links.label_id )')
+    end
+  end
+
+  def up
+    # Some of these queries can take up to 10 seconds to run on GitLab.com,
+    # which is pretty close to our 15 second statement timeout. To ensure a
+    # smooth deployment procedure we disable the statement timeouts for this
+    # migration, just in case.
+    disable_statement_timeout do
+      # On GitLab.com there are over 2,000,000 orphaned label links. On
+      # staging, removing 100,000 rows generated a max replication lag of 6.7
+      # MB. In total, removing all these rows will only generate about 136 MB
+      # of data, so it should be safe to do this.
+      LabelLinks.orphaned.each_batch(of: 100_000) do |batch|
+        batch.delete_all
+      end
+    end
+
+    add_concurrent_foreign_key(:label_links, :labels, column: :label_id, on_delete: :cascade)
+  end
+
+  def down
+    # There is no way to restore orphaned label links.
+    if foreign_key_exists?(:label_links, column: :label_id)
+      remove_foreign_key(:label_links, column: :label_id)
+    end
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index a417d0bc70a..98ae9f7b131 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -2357,6 +2357,7 @@ ActiveRecord::Schema.define(version: 20180906101639) do
   add_foreign_key "issues", "users", column: "author_id", name: "fk_05f1e72feb", on_delete: :nullify
   add_foreign_key "issues", "users", column: "closed_by_id", name: "fk_c63cbf6c25", on_delete: :nullify
   add_foreign_key "issues", "users", column: "updated_by_id", name: "fk_ffed080f01", on_delete: :nullify
+  add_foreign_key "label_links", "labels", name: "fk_d97dd08678", on_delete: :cascade
   add_foreign_key "label_priorities", "labels", on_delete: :cascade
   add_foreign_key "label_priorities", "projects", on_delete: :cascade
   add_foreign_key "labels", "namespaces", column: "group_id", on_delete: :cascade
diff --git a/spec/migrations/remove_orphaned_label_links_spec.rb b/spec/migrations/remove_orphaned_label_links_spec.rb
new file mode 100644
index 00000000000..13b8919343e
--- /dev/null
+++ b/spec/migrations/remove_orphaned_label_links_spec.rb
@@ -0,0 +1,40 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+require Rails.root.join('db', 'post_migrate', '20180906051323_remove_orphaned_label_links.rb')
+
+describe RemoveOrphanedLabelLinks, :migration do
+  let(:label_links) { table(:label_links) }
+  let(:labels) { table(:labels) }
+
+  let(:project) { create(:project) } # rubocop:disable RSpec/FactoriesInMigrationSpecs
+  let(:label) { create_label }
+
+  context 'add foreign key on label_id' do
+    let!(:label_link_with_label) { create_label_link(label_id: label.id) }
+    let!(:label_link_without_label) { create_label_link(label_id: nil) }
+
+    it 'removes orphaned labels without corresponding label' do
+      expect { migrate! }.to change { LabelLink.count }.from(2).to(1)
+    end
+
+    it 'does not remove entries with valid label_id' do
+      expect { migrate! }.not_to change { label_link_with_label.reload }
+    end
+  end
+
+  def create_label(**opts)
+    labels.create!(
+      project_id: project.id,
+      **opts
+    )
+  end
+
+  def create_label_link(**opts)
+    label_links.create!(
+      target_id: 1,
+      target_type: 'Issue',
+      **opts
+    )
+  end
+end