diff --git a/changelogs/unreleased/4525-fix-project-indexes.yml b/changelogs/unreleased/4525-fix-project-indexes.yml
new file mode 100644
index 00000000000..930e3b934c2
--- /dev/null
+++ b/changelogs/unreleased/4525-fix-project-indexes.yml
@@ -0,0 +1,5 @@
+---
+title: Rework some projects table indexes around repository_storage field
+merge_request: 20377
+author:
+type: fixed
diff --git a/db/post_migrate/20180704145007_update_project_indexes.rb b/db/post_migrate/20180704145007_update_project_indexes.rb
new file mode 100644
index 00000000000..193563b36db
--- /dev/null
+++ b/db/post_migrate/20180704145007_update_project_indexes.rb
@@ -0,0 +1,23 @@
+# See http://doc.gitlab.com/ce/development/migration_style_guide.html
+# for more information on how to write migrations for GitLab.
+
+class UpdateProjectIndexes < ActiveRecord::Migration
+  include Gitlab::Database::MigrationHelpers
+
+  DOWNTIME = false
+  NEW_INDEX_NAME = 'idx_project_repository_check_partial'
+
+  disable_ddl_transaction!
+
+  def up
+    add_concurrent_index(:projects,
+      [:repository_storage, :created_at],
+      name: NEW_INDEX_NAME,
+      where: 'last_repository_check_at IS NULL'
+    )
+  end
+
+  def down
+    remove_concurrent_index_by_name(:projects, NEW_INDEX_NAME)
+  end
+end
diff --git a/db/schema.rb b/db/schema.rb
index d2aa31fae30..1a5555fb3a4 100644
--- a/db/schema.rb
+++ b/db/schema.rb
@@ -1674,6 +1674,7 @@ ActiveRecord::Schema.define(version: 20180704204006) do
   add_index "projects", ["path"], name: "index_projects_on_path", using: :btree
   add_index "projects", ["path"], name: "index_projects_on_path_trigram", using: :gin, opclasses: {"path"=>"gin_trgm_ops"}
   add_index "projects", ["pending_delete"], name: "index_projects_on_pending_delete", using: :btree
+  add_index "projects", ["repository_storage", "created_at"], name: "idx_project_repository_check_partial", where: "(last_repository_check_at IS NULL)", using: :btree
   add_index "projects", ["repository_storage"], name: "index_projects_on_repository_storage", using: :btree
   add_index "projects", ["runners_token"], name: "index_projects_on_runners_token", using: :btree
   add_index "projects", ["star_count"], name: "index_projects_on_star_count", using: :btree