Jerusalem is a town in Yates County, New York, United States. The population was 4,469 at the 2010 census. The town is named after th…Jerusalem is a town in Yates County, New York, United States. The population was 4,469 at the 2010 census. The town is named after the ancient city of Jerusalem. The Town of Jerusalem is on the south border of the county and is southwest of Geneva, New York.