Why would your stomach hurt when you pee?

Infection is likely: Lower abdominal pain while urinating suggests urine infection especially when associated with frequency of urination of small volumes of smelly urine. Urinalysis will confirm or refute this.

Bladder pain: is often felt in the lower abdomen (or "stomach") and usually this is a sign of bladder infection (In males prostate infection (prostatitis) may produce lower abdominal pain. A urinalysis/culture along with an in person visit to your PCP is strongly suggested! Hope this is helpful Dr X

Cystitis?: Pain with bladder filling and relief with voiding is a symptom bladder inflammation. See your primary physician and get a urinalysis, to start the work-up. In the mean time drink more water and avoid bladder irritants such as caffeine, nicotine, spicy and acidic foods.