Penn Yan is an incorporated village in Yates County, New York, United States. The population was 5,159 at the 2010 census. It is the county seat of Yates County and lies at the north end of the east branch of Keuka Lake, one of the Finger Lakes.The Village of Penn Yan is primarily in the Town of Milo, but a small section is in the Town of Benton. A smaller section is in the Town of Jerusalem. The Penn Yan Airport is south of the village. The name "Penn Yan" is a syllabic abbreviation of "Pennsylvania Yankee". It houses the Penn Yan Central School District.