I'm working on a site that deals with banner serving, so users sign up and trade banner impressions/clicks.

My problem is this: Say a user places my banner code on their site which displays random banners.

Then a visitor comes by, clicks on the banner on Site1 which takes him to Site2 through http://myexchangesite.com/linkout.php?bannerid

The problem lies when the webmaster of Site2 that is receiving the visit is seeing in his Google Analytics that the referral came from Site1 rather than from my banner serving site even though when a user clicks on a link they're actually clicking on http://myexchangesite.com/linkout.php rather than the direct URL to Site2.

In the file linkout.php, there is a server redirect:
header ("Location: $_GET[url]");

How do I change this so that the referring site becomes my exchange site rather than the site where they clicked the banner?

Thanks

You can't.

A website cannot set or change referrer headers, ONLY the client browser can set the referrer.

I understand that, but how can I change the redirect code so that the user ends up actually visiting myexchangesite.com/linkout.php so then the referrer is myexchangesite rather than just a redirector of traffic?

have them land on the page, and they will have to click again. It's the "click" that sets the referrer field.

And document.referrer is a read only property for javascript.

About the only option available to you will be to use a 302 redirect which should drop the referrer field, then add a url parameter (querystring) to the target URI for the recipient site to track.