Wagoner is a city in Wagoner County, Oklahoma, United States. The population was 8,323 at the 2010 census, compared to the figure of 7…Wagoner is a city in Wagoner County, Oklahoma, United States. The population was 8,323 at the 2010 census, compared to the figure of 7,669 recorded in 2000. It is the county seat of Wagoner County. Wagoner became the first city incorporated in Indian Territory on January 4, 1896.