I'm not sure that you can take a train from Girona to Perpignan. I go to Perpignan regularly and as far as I'm aware there's no train to/from Girona. There's no train to Barcelona either, and there won't be one until 2009 when a newly laid TGV line will connect the two cities. The reason is that the Iberian peninsula operates with a different rail gauge to most of the rest of Europe. "Protocol" is right, the only way to go by train is to take two trains, one from Girona to the border, and one from the border to Perpignan. The problem is that there's a distance between the most northerly Spanish station and the most southerly French one. I don't know if there's a connecting bus.
You might consider hiring a car in Girona and drive up. Perpignan is about 90 minutes away and its a very direct route.