diff --git a/sql/sql_parse.cc b/sql/sql_parse.cc
index 72630822ad4..6baff31537a 100644
--- a/sql/sql_parse.cc
+++ b/sql/sql_parse.cc
@@ -1082,9 +1082,20 @@ void do_handle_bootstrap(THD *thd)
 end:
   in_bootstrap= FALSE;
   delete thd;
+  if (!opt_bootstrap)
+  {
+    /*
+      We need to wake up main thread in case of read_init_file().
+      This is not done by THD::~THD() when there are other threads running
+      (binlog background thread, for example). So do it here again.
+    */
+    mysql_mutex_lock(&LOCK_thread_count);
+    mysql_cond_broadcast(&COND_thread_count);
+    mysql_mutex_unlock(&LOCK_thread_count);
+  }
 
 #ifndef EMBEDDED_LIBRARY
-  DBUG_ASSERT(thread_count == 0);
+  DBUG_ASSERT(!opt_bootstrap || thread_count == 0);
   my_thread_end();
   pthread_exit(0);
 #endif