I'm allergic to penicillin, my girlfriend has been taking penicillin antibiotics for a surgery, will it affect me while having sex?

No but . . .: The fact that one partner takes medication to which other is allergic really shouldn't impact allergic partner, assuming that all traces have been wipe away especially if anaphylactic response. However, it's always a great idea to practice protected (safer) sex eg wear a condom each & every time to minimize transmission of stds.

Possible: Penicillin allergy from sexual contact has been reported although it must be rare as I have not seen a patient reporting this problem. If you have anaphylaxis to penicillin, you should use a condom until 48 hrs after she has completed the course of penicillin just to be safe. If the reaction is just a skin rash , it would be your choice to use condom or not.