Junction City is a city in and the county seat of Geary County, Kansas, United States. As of the 2020 census, the population of the city was …Junction City is a city in and the county seat of Geary County, Kansas, United States. As of the 2020 census, the population of the city was 22,932. Fort Riley, a major U.S. Army post, is nearby. Junction City is so named from its position at the confluence of the Smoky Hill and Republican rivers, which forms the Kansas River.