That's odd to have them at night only. Is it because there is no food in your system (e.g., maybe you eat an early dinner and there's absolutely nothing left?) If so, it could be the low-blood sugar from nothing in your stomach that could be causing the night headaches......
Maybe try a little protein snack an hour before the headaches are coming.
I am plagued by headaches all the time (regardless of whether I'm dieting or not), so I know how nasty it is to get one before bed when you need to relax and unwind. I have put on one of those eye masks over my eyes to block out any light, and put a hot/damp washcloth on my head to ease the pain in bed. (Excedrin Migraine works pretty well too). Good luck and let me know if they are continuing - you may have to hit the Dr.s office if they continue in frequency.