diff --git src/wp-includes/theme.php src/wp-includes/theme.php
index 406fa4a310..b86b5f1611 100644
--- src/wp-includes/theme.php
+++ src/wp-includes/theme.php
@@ -410,6 +410,8 @@ function register_theme_directory( $directory ) {
 		$wp_theme_directories[] = $untrailed;
 	}
 
+	delete_site_transient( 'theme_roots' );
+
 	return true;
 }