diff --git a/src/applications/repository/engine/PhabricatorRepositoryPullEngine.php b/src/applications/repository/engine/PhabricatorRepositoryPullEngine.php
--- a/src/applications/repository/engine/PhabricatorRepositoryPullEngine.php
+++ b/src/applications/repository/engine/PhabricatorRepositoryPullEngine.php
@@ -353,13 +353,56 @@
     // Load the refs we're planning to fetch from the remote repository.
     $remote_refs = $this->loadGitRemoteRefs(
       $repository,
-      $repository->getRemoteURIEnvelope());
+      $repository->getRemoteURIEnvelope(),
+      $is_local = false);
 
     // Load the refs we're planning to fetch from the local repository, by
     // using the local working copy path as the "remote" repository URI.
     $local_refs = $this->loadGitRemoteRefs(
       $repository,
-      new PhutilOpaqueEnvelope($path));
+      new PhutilOpaqueEnvelope($path),
+      $is_local = true);
+
+    // See T13448. The "git fetch --prune ..." flag only prunes local refs
+    // matching the refspecs we pass it. If "Fetch Refs" is configured, we'll
+    // pass it a very narrow list of refspecs, and it won't prune older refs
+    // that aren't currently subject to fetching.
+
+    // Since we want to prune everything that isn't (a) on the fetch list and
+    // (b) in the remote, handle pruning of any surplus leftover refs ourselves
+    // before we fetch anything.
+
+    // (We don't have to do this if "Fetch Refs" isn't set up, since "--prune"
+    // will work in that case, but it's a little simpler to always go down the
+    // same code path.)
+
+    $surplus_refs = array();
+    foreach ($local_refs as $local_ref => $local_hash) {
+      $remote_hash = idx($remote_refs, $local_ref);
+      if ($remote_hash === null) {
+        $surplus_refs[] = $local_ref;
+      }
+    }
+
+    if ($surplus_refs) {
+      $this->log(
+        pht(
+          'Found %s surplus local ref(s) to delete.',
+          phutil_count($surplus_refs)));
+      foreach ($surplus_refs as $surplus_ref) {
+        $this->log(
+          pht(
+            'Deleting surplus local ref "%s" ("%s").',
+            $surplus_ref,
+            $local_refs[$surplus_ref]));
+
+        $repository->execLocalCommand(
+          'update-ref -d %R --',
+          $surplus_ref);
+
+        unset($local_refs[$surplus_ref]);
+      }
+    }
 
     if ($remote_refs === $local_refs) {
       $this->log(
@@ -378,7 +421,7 @@
     // checked out. See T13280.
 
     $future = $repository->getRemoteCommandFuture(
-      'fetch --prune --update-head-ok -- %P %Ls',
+      'fetch --update-head-ok -- %P %Ls',
       $repository->getRemoteURIEnvelope(),
       $fetch_rules);
 
@@ -474,21 +517,32 @@
 
   private function loadGitRemoteRefs(
     PhabricatorRepository $repository,
-    PhutilOpaqueEnvelope $remote_envelope) {
+    PhutilOpaqueEnvelope $remote_envelope,
+    $is_local) {
 
-    $ref_rules = $this->getGitRefRules($repository);
+    // See T13448. When listing local remotes, we want to list everything,
+    // not just refs we expect to fetch. This allows us to detect that we have
+    // undesirable refs (which have been deleted in the remote, but are still
+    // present locally) so we can update our state to reflect the correct
+    // remote state.
 
-    // NOTE: "git ls-remote" does not support "--" until circa January 2016.
-    // See T12416. None of the flags to "ls-remote" appear dangerous, but
-    // refuse to list any refs beginning with "-" just in case.
+    if ($is_local) {
+      $ref_rules = array();
+    } else {
+      $ref_rules = $this->getGitRefRules($repository);
 
-    foreach ($ref_rules as $ref_rule) {
-      if (preg_match('/^-/', $ref_rule)) {
-        throw new Exception(
-          pht(
-            'Refusing to list potentially dangerous ref ("%s") beginning '.
-            'with "-".',
-            $ref_rule));
+      // NOTE: "git ls-remote" does not support "--" until circa January 2016.
+      // See T12416. None of the flags to "ls-remote" appear dangerous, but
+      // refuse to list any refs beginning with "-" just in case.
+
+      foreach ($ref_rules as $ref_rule) {
+        if (preg_match('/^-/', $ref_rule)) {
+          throw new Exception(
+            pht(
+              'Refusing to list potentially dangerous ref ("%s") beginning '.
+              'with "-".',
+              $ref_rule));
+        }
       }
     }