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
@@ -8,6 +8,7 @@
 use Drupal\Component\Plugin\Exception\PluginNotFoundException;
 use Drupal\Core\Block\BlockPluginInterface;
 use Drupal\Core\Cache\Cache;
+use Drupal\Core\Database\DatabaseExceptionWrapper;
 use Drupal\Core\Entity\Query\QueryException;
 use Drupal\Core\Extension\Extension;
 use Drupal\Core\Extension\ExtensionDiscovery;
@@ -1053,7 +1054,7 @@
             // would be required before being able to uninstall them.
             if ($entity_type->getProvider() != $module_name && $entity_type->isFieldable()) {
               try {
-                $query = \Drupal::entityQuery($entity_type_id);
+                $has_data = \Drupal::entityQuery($entity_type_id)->count()->execute();
               }
               catch (QueryException $e) {
                 // If an entity type can't be queried, treat it has having no
@@ -1061,9 +1062,19 @@
                 // to be uninstalled.
                 // @todo Require all storage handlers to support querying:
                 //   https://www.drupal.org/node/2337753.
-                $query = NULL;
+                $has_data = FALSE;
               }
-              if ($query && $query->count()->execute()) {
+              catch (DatabaseExceptionWrapper $e) {
+                // During KernelTestBase tests, some entity schema are not
+                // installed.
+                if (!\Drupal::database()->schema()->tableExists($entity_type->getBaseTable())) {
+                  $has_data = FALSE;
+                }
+                else {
+                  throw $e;
+                }
+              }
+              if ($has_data) {
                 foreach ($entity_manager->getFieldStorageDefinitions($entity_type_id) as $storage_definition) {
                   if ($storage_definition->getProvider() == $module_name) {
                     $info['required'] = TRUE;