diff --git a/src/applications/repository/engine/PhabricatorRepositoryDiscoveryEngine.php b/src/applications/repository/engine/PhabricatorRepositoryDiscoveryEngine.php
--- a/src/applications/repository/engine/PhabricatorRepositoryDiscoveryEngine.php
+++ b/src/applications/repository/engine/PhabricatorRepositoryDiscoveryEngine.php
@@ -93,6 +93,8 @@
     // Clear the working set cache.
     $this->workingSet = array();
 
+    $task_priority = $this->getImportTaskPriority($repository, $refs);
+
     // Record discovered commits and mark them in the cache.
     foreach ($refs as $ref) {
       $this->recordCommit(
@@ -100,7 +102,8 @@
         $ref->getIdentifier(),
         $ref->getEpoch(),
         $ref->getCanCloseImmediately(),
-        $ref->getParents());
+        $ref->getParents(),
+        $task_priority);
 
       $this->commitCache[$ref->getIdentifier()] = true;
     }
@@ -536,7 +539,8 @@
     $commit_identifier,
     $epoch,
     $close_immediately,
-    array $parents) {
+    array $parents,
+    $task_priority) {
 
     $commit = new PhabricatorRepositoryCommit();
     $conn_w = $repository->establishConnection('w');
@@ -559,7 +563,7 @@
         $commit_identifier);
 
       // After reviving a commit, schedule new daemons for it.
-      $this->didDiscoverCommit($repository, $commit, $epoch);
+      $this->didDiscoverCommit($repository, $commit, $epoch, $task_priority);
       return;
     }
 
@@ -620,7 +624,7 @@
         }
       $commit->saveTransaction();
 
-      $this->didDiscoverCommit($repository, $commit, $epoch);
+      $this->didDiscoverCommit($repository, $commit, $epoch, $task_priority);
 
       if ($this->repairMode) {
         // Normally, the query should throw a duplicate key exception. If we
@@ -648,9 +652,10 @@
   private function didDiscoverCommit(
     PhabricatorRepository $repository,
     PhabricatorRepositoryCommit $commit,
-    $epoch) {
+    $epoch,
+    $task_priority) {
 
-    $this->insertTask($repository, $commit);
+    $this->insertTask($repository, $commit, $task_priority);
 
     // Update the repository summary table.
     queryfx(
@@ -677,6 +682,7 @@
   private function insertTask(
     PhabricatorRepository $repository,
     PhabricatorRepositoryCommit $commit,
+    $task_priority,
     $data = array()) {
 
     $vcs = $repository->getVersionControlSystem();
@@ -696,27 +702,6 @@
 
     $data['commitID'] = $commit->getID();
 
-    // If the repository is importing for the first time, we schedule tasks
-    // at IMPORT priority, which is very low. Making progress on importing a
-    // new repository for the first time is less important than any other
-    // daemon task.
-
-    // If the repository has finished importing and we're just catching up
-    // on recent commits, we schedule discovery at COMMIT priority, which is
-    // slightly below the default priority.
-
-    // Note that followup tasks and triggered tasks (like those generated by
-    // Herald or Harbormaster) will queue at DEFAULT priority, so that each
-    // commit tends to fully import before we start the next one. This tends
-    // to give imports fairly predictable progress. See T11677 for some
-    // discussion.
-
-    if ($repository->isImporting()) {
-      $task_priority = PhabricatorWorker::PRIORITY_IMPORT;
-    } else {
-      $task_priority = PhabricatorWorker::PRIORITY_COMMIT;
-    }
-
     $options = array(
       'priority' => $task_priority,
     );
@@ -934,4 +919,71 @@
       $data['epoch']);
   }
 
+  private function getImportTaskPriority(
+    PhabricatorRepository $repository,
+    array $refs) {
+
+    // If the repository is importing for the first time, we schedule tasks
+    // at IMPORT priority, which is very low. Making progress on importing a
+    // new repository for the first time is less important than any other
+    // daemon task.
+
+    // If the repository has finished importing and we're just catching up
+    // on recent commits, we usually schedule discovery at COMMIT priority,
+    // which is slightly below the default priority.
+
+    // Note that followup tasks and triggered tasks (like those generated by
+    // Herald or Harbormaster) will queue at DEFAULT priority, so that each
+    // commit tends to fully import before we start the next one. This tends
+    // to give imports fairly predictable progress. See T11677 for some
+    // discussion.
+
+    if ($repository->isImporting()) {
+      $this->log(
+        pht(
+          'Importing %s commit(s) at low priority ("PRIORITY_IMPORT") '.
+          'because this repository is still importing.',
+          phutil_count($refs)));
+
+      return PhabricatorWorker::PRIORITY_IMPORT;
+    }
+
+    // See T13369. If we've discovered a lot of commits at once, import them
+    // at lower priority.
+
+    // This is mostly aimed at reducing the impact that synchronizing thousands
+    // of commits from a remote upstream has on other repositories. The queue
+    // is "mostly FIFO", so queueing a thousand commit imports can stall other
+    // repositories.
+
+    // In a perfect world we'd probably give repositories round-robin queue
+    // priority, but we don't currently have the primitives for this and there
+    // isn't a strong case for building them.
+
+    // Use "a whole lot of commits showed up at once" as a heuristic for
+    // detecting "someone synchronized an upstream", and import them at a lower
+    // priority to more closely approximate fair scheduling.
+
+    if (count($refs) >= PhabricatorRepository::LOWPRI_THRESHOLD) {
+      $this->log(
+        pht(
+          'Importing %s commit(s) at low priority ("PRIORITY_IMPORT") '.
+          'because many commits were discovered at once.',
+          phutil_count($refs)));
+
+      return PhabricatorWorker::PRIORITY_IMPORT;
+    }
+
+    // Otherwise, import at normal priority.
+
+    if ($refs) {
+      $this->log(
+        pht(
+          'Importing %s commit(s) at normal priority ("PRIORITY_COMMIT").',
+          phutil_count($refs)));
+    }
+
+    return PhabricatorWorker::PRIORITY_COMMIT;
+  }
+
 }
diff --git a/src/applications/repository/storage/PhabricatorRepository.php b/src/applications/repository/storage/PhabricatorRepository.php
--- a/src/applications/repository/storage/PhabricatorRepository.php
+++ b/src/applications/repository/storage/PhabricatorRepository.php
@@ -34,6 +34,8 @@
    */
   const IMPORT_THRESHOLD = 7;
 
+  const LOWPRI_THRESHOLD = 64;
+
   const TABLE_PATH = 'repository_path';
   const TABLE_PATHCHANGE = 'repository_pathchange';
   const TABLE_FILESYSTEM = 'repository_filesystem';