In 1880, a tiny town by the name of Wano was founded. This town was located in the Northwest corner of Kansas in the Cheyenne Township, part of Rawlins County.

In 1885, Kansas passed a herd law whereby the large cattle ranchers could no longer let their cattle run on the open range. It was about this time that people from the east became interested in the northwestern part of the state and settled in the area. It was during this time the town of Bird City was begun. The town was named for Benjamin Bird, a manager of the Northwest Cattle Company, whose headquarters were twenty miles north of the new town. (In March 1885, there were 204 people in the territory - by March 1886, there were 1256 people in the territory.)

On April 1, 1886 , Governor John A. Martin issued a proclamation declaring that the unorganized county of Cheyenne was to become a bona fide county. (It was named after the Cheyenne Indians that roamed the western plain at that time.) The Governor designated Bird City as the temporary county seat.

The original settlement in the county, Wano, was a trading post (located about one and one half miles northeast of where St. Francis is now located). Wano was an island town, so everything had to be freighted in by horses, mules and oxen from the towns of Haigler and Benkelman, located in Nebraska.

The railroad dream was becoming a reality in 1887. The grade survey stakes were even put in place and the site for the depot was chosen. (Located on the south side of Wano) Captain A.L. Emerson, an employee of the Lincoln Land Co., was instrumental in getting the railroad built at the present location. (The Lincoln Land Co. was known for purchasing land near proposed railroads and starting new towns on their land.) Captain Emerson was owner of the Log Chip Ranch which was located one and one half miles south of Wano (where St. Francis is now located), and was making serveral trips to Lincoln, Nebraska. The citizens believed he was convincing the railroad to have Wano become a division station. At the time, the citizens assumed that the railroad would continue on to Pueblo, Colorado. This assumption was dashed when a representative of the Lincoln Land Company came to Wano in July and pulled all the stakes up. By November, the land company told the citizens that if they would "move out where we want you to, we will give you a round house and make the NEW Wano a division station."

In late November, the new town site was surveyed and plotted. The people of Wano decided to accept lots in the new town and free transportation for their buildings to be moved to the new site. The actual move to the new site began December 5, 1887, and the last building moved from Wano on May 2, 1888 .

The new town was named St. Francis. The actual origin of the name is unknown, but there are three theories: 1) For Fannie, the wife of Captain Emerson, 2) For Frank, the deceased brother of Captain Emerson, or 3) For J. Francis, an official of the railroad.

On March 2, 1889, the County Commissioners met to canvas the county for the election which would decide the permanent county seat. St. Francis was elected to be the county seat. On June 3, 1903 , the city of St. Francis was incorporated.

On May 31, 1935, the Republican River, which flows by St. Francis and through the northwestern part of the county, reached its highest crest in history. Nineteen persons lost their lives in the worst flood of the county's history. Flood waters that were a mile to a mile and a half wide swept past St. Francis at 3:00 a.m. They cleared the valley of buildings, bridges, trees and highways, as the flood coursed a new path diagonally across the county.