If you mean the part of the body containing the stomach; belly or abdomen. You can say おなかがいたい．おなかが痛い． If you mean particularly organ, stomach. You can say いがいたい．胃が痛い．

わたし　の　おなか　が　いたい。watashi no onaka ga itai. You can skip the "watashi no" and just say "Onaka ga itai" Onaka(お腹) means stomach, or abdomen. And itai(痛い) means hurts. :)