Remember that PhP is a server side language, using the server/client model, if you want to display something to the user, you need to pass data to client, then display that data using a client side language.
For this, I recommend using a javascript countdown.
An example of passing the information between client and server would be like so:
<?php
if (isset($_COOKIE["user"]))
{
$setTimer = "true";
}
?>
And your javascript..
var setTimer = "<?php Print($setTimer); ?>";
if(setTimer)
{
DisplayATimer
}
If you're looking for a javascript timer, and are unsure how to make one, I'm sure there's a few you can grab if you google around. It's also worth noting that javascript has full access to cookies, as they're stored locally. So unless you need to do something with your PhP, it may be better to just check for the cookie within javascript.
How do I set/unset cookie with jQuery? This post is helpful in that regard.