Index: src/wp-includes/js/customize-preview.js
===================================================================
--- src/wp-includes/js/customize-preview.js	(revision 40055)
+++ src/wp-includes/js/customize-preview.js	(working copy)
@@ -147,8 +147,8 @@
 
 			isInternalJumpLink = ( '#' === link.attr( 'href' ).substr( 0, 1 ) );
 
-			// Allow internal jump links to behave normally without preventing default.
-			if ( isInternalJumpLink ) {
+			// Allow internal jump links and JS links to behave normally without preventing default.
+			if ( isInternalJumpLink || 'javascript:' === link.prop( 'protocol' ) ) { // jshint ignore:line
 				return;
 			}
 
@@ -335,7 +335,7 @@
 		}
 
 		// Ignore links with href="#" or href="#id".
-		if ( '#' === $( element ).attr( 'href' ).substr( 0, 1 ) ) {
+		if ( '#' === $( element ).attr( 'href' ).substr( 0, 1 ) || 'javascript:' === element.protocol ) { // jshint ignore:line
 			return;
 		}