Don't know if these suggestions will help, but I have had a similar situation, and there are a few possibilities.
First of all, it may simply be a case of positioning. The shape/size of your equipment may not fit the shape/size of her equipment in the manner that you're trying it. (you could be pushing against an ovary in the position that you're in, which can be very painful, or you/she might have a curve that's hitting the wrong spot) She may be more comfortable if you lay on your back and let her take the top, that way she can control how quickly there is penetration and how deeply, and adjust her angle. You can try many different positions, and it is fun to experiment. There are several websites out there that describe a variety of positions- do a google search on sexual positions or sexual positions during pregnancy (since this will also give you positions that are most comfortable for women who have pain).
Also make sure you've spent some time on foreplay, because women's bodies need warm-up time inside as well as out.
If you've tried these things and it still is painful for your girlfriend, there is a possibility that there may be something else going on. Encourage her to see a gynecologist that she would feel comfortable talking to, and have an examination. I had this problem as well as several other symptoms, and eventually was diagnosed with endometriosis (though I'm not suggesting at ALL that she has this problem. Worth checking out if she continues to have pain though).
Hope things get more fun and comfortable for you both.