Specifying the type as iframe
seems to make it work.
$( document ).ready(function() {
$( ".youtube_box" ).click(function() {
var YouTubeID = this.id;
$.fancybox({
href : 'https://www.youtube.com/embed/' + YouTubeID + '?autoplay=1'
}, {
type: 'iframe'
});
});
});
See this Fiddle.