If a prayer is distracting in the classroom, I think it would be best for the student to pray outside the classroom before the test begins, during a 5 minute "get to your next class" period in the hallway, outside during lunch, etc. Anything that distracts during the test - whether based in religion or not - should not be allowed.

But if you're just praying silently during the test? I don't see any problem with that.