In 1855 the Kansas Territorial Legislature set the boundary for a portion of land west of Shawnee County and named it Richardson county after William P. Richardson, a strongly pro-slavery member of the Kansas Territorial Council in 1855. The county was attached to Shawnee County for business and judicial purposes and had no officers of record until 1859.
In the early days of the county, most settlements were in the present day Wilmington and Wabaunsee townships. In 1856, a colony of abolitionists from New Haven, Connecticut, known as the Beecher Bible and Rifle Colony, settled near the Kaw River where a town site called Wabaunsee had been previously laid out. Wabaunsee was the name of a famous Potawatomie Chief and meant "Dawn of Day" in the Indian language.
In 1859 residents from this area petitioned the Free State Legislature at Topeka to change the name of the county to Wabaunsee and they did so. That same year County officers were elected, commisioner districts were formed and Wabaunsee was designated the county seat. In 1866, after two elections the county seat was moved to Alma in January of 1867, and has remained there since.
Wabaunsee County currently has seven incorporated cities: Alma, Alta Vista, Eskridge, Harveyville, Maple Hill, McFarland and Paxico.