diff -u b/core/modules/system/src/Controller/SystemController.php b/core/modules/system/src/Controller/SystemController.php
--- b/core/modules/system/src/Controller/SystemController.php
+++ b/core/modules/system/src/Controller/SystemController.php
@@ -189,6 +189,7 @@
     //  Clean up the bootstrap "missing files" cache when listing themes.
     if (\Drupal::hasService('cache.bootstrap')) {
       \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
+      drupal_static_reset('drupal_get_filename:missing');
     }
 
     $config = $this->config('system.theme');
diff -u b/core/modules/system/src/Form/ModulesListForm.php b/core/modules/system/src/Form/ModulesListForm.php
--- b/core/modules/system/src/Form/ModulesListForm.php
+++ b/core/modules/system/src/Form/ModulesListForm.php
@@ -177,6 +177,7 @@
     //  Clean up the "missing files" cache when listing modules.
     if (\Drupal::hasService('cache.bootstrap')) {
       \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
+      drupal_static_reset('drupal_get_filename:missing');
     }
 
     $form['filters'] = array(
diff -u b/core/modules/system/system.module b/core/modules/system/system.module
--- b/core/modules/system/system.module
+++ b/core/modules/system/system.module
@@ -1204,6 +1204,7 @@
   // Clean up the bootstrap "missing files" cache when running cron.
   if (\Drupal::hasService('cache.bootstrap')) {
     \Drupal::cache('bootstrap')->invalidate('drupal_get_filename:missing');
+    drupal_static_reset('drupal_get_filename:missing');
   }
 
   // Clean up the expirable key value database store.