diff --git a/src/wp-includes/theme.php b/src/wp-includes/theme.php
index ecbedec482..662df894b3 100644
--- a/src/wp-includes/theme.php
+++ b/src/wp-includes/theme.php
@@ -413,6 +413,8 @@ function register_theme_directory( $directory ) {
 		$wp_theme_directories[] = $untrailed;
 	}
 
+	wp_clean_themes_cache();
+
 	return true;
 }
 
diff --git a/tests/phpunit/tests/theme/themeDir.php b/tests/phpunit/tests/theme/themeDir.php
index 2cab375b1a..4e915aeb40 100644
--- a/tests/phpunit/tests/theme/themeDir.php
+++ b/tests/phpunit/tests/theme/themeDir.php
@@ -293,4 +293,24 @@ class Tests_Theme_ThemeDir extends WP_UnitTestCase {
 		rmdir( WP_CONTENT_DIR . '/themes/foo' );
 		rmdir( WP_CONTENT_DIR . '/themes/foo-themes' );
 	}
+
+	/**
+	 * @ticket 43228
+	 */
+	function test_theme_dir_caches() {
+		@mkdir( WP_CONTENT_DIR . '/themes/foo' );
+		@mkdir( WP_CONTENT_DIR . '/themes/foo/bar' );
+
+		$old_roots = get_theme_roots();
+
+		register_theme_directory( WP_CONTENT_DIR . '/themes/foo' );
+
+		$new_roots = get_theme_roots();
+
+		rmdir( WP_CONTENT_DIR . '/themes/foo/bar' );
+		rmdir( WP_CONTENT_DIR . '/themes/foo' );
+
+		$this->assertNotEquals( $new_roots, $old_roots );
+		$this->assertArrayHasKey( 'foo', $new_roots );
+	}
 }