Saint-Aubin-sur-Yonne (, literally Saint-Aubin on Yonne) is a commune in the Yonne department in Bourgogne-Franche-Comté in north-central France. It is part of the canton of Joigny and the arrondissement of Sens. The inhabitants of Saint-Aubin-sur-Yonne called the Aubinois. The area is 8.9 square kilometers and the population is 434 (2023). It is located at an altitude of 92 meters.