The village is near the junction of U.S. Highway 550 and NM Highway 4, at the south end of the Jemez Valley. The Jemez River runs through San Ysidro, just north of where the Rio Salado River joins the Jemez River.
The village has been a farming community since 1699 when Juan Trujillo established a settlement named for San Ysidro, or Saint Isidore the Farmer. The Village was incorporated in 1967. An annual San Ysidro Fiesta Day is held each year in mid-May.