Pawnee City is a city in and the county seat of Pawnee County, Nebraska, United States. The population was 878 at the 2010 census. The site …Pawnee City is a city in and the county seat of Pawnee County, Nebraska, United States. The population was 878 at the 2010 census. The site of present-day Pawnee City was designated as the county seat on November 4, 1856, and the townsite was platted in the spring of 1857. Pawnee City was incorporated in 1858, and is named after the Pawnee Native Americans.