You'll have to pass the current server time into the page as it's created, and use that to initialize your javascript clock. Thankfully, JS's Date object will accept a timestamp (in milliseconds) to initalize with, so it's as simple as:
<script type="text/javascript">
var d = new Date(<?php echo time() * 1000 ?>);
</script>
Note the * 1000
part. PHP's timestamps are in seconds, and JS's are in milliseconds.