Refers to the lower belly or the area around the stomach. Often used in expressions like 小腹が空く (to be slightly hungry) or 小腹が痛い (to have a stomachache).
I was a little hungry, so I ate a rice ball.
My stomach has been hurting since this morning.
Compound of 小 (small) and 腹 (belly). The exact historical derivation is uncertain, but it likely originated as a colloquial term for the lower abdomen or a mild stomach sensation.