Troy is a city in and the county seat of Doniphan County, Kansas, United States. As of the 2020 census, the population of the city was 964.

Doniphan County is the most northeastern county in the U.S. state of Kansas. Its county seat is Troy, and its most populous city is Wathena. As of the 2020 census, the county population was 7,510. The county was named after Alexander Doniphan, a Mexican–American War hero. It is bounded on the east by the Missouri river, south by Atchison county, and west by Brown county.