Shawnee is named for the Shawnee Indians that were relocated here in the late 1820s. The westward push of white settlement had weakened and geographically divided the Shawnees by 1825 when the first of three treaties forced them to relocate to Kansas. Here they found an abundance of timber and free-flowing springs. Because the Shawnee wisely lined the springs with gum tree logs to keep them free of contaminating silt, the settlement was called Gum Springs.

In an 1825 treaty with the Indians, the U.S. government gave the Shawnee Indians 1,600,000 acres of land in eastern Kansas, including all of Johnson County, in exchange for their lands in Missouri. By 1854, a new treaty was negotiated, with the Indians selling back to the United States all of the land with the exception of 200,000 acres reserved for their homes, amounting to 200 acres for each member of the tribe. In 1854 the Kansas Territory was opened for settlement. The newly repossessed territory was sold by the government to the incoming home-seekers. Shawneetown (later shortened to Shawnee) was platted soon after in 1856.

One of the State's earliest towns, Shawnee was also the site of the first territorial legislature, and home to the first territorial governor. Located at the intersection of early military and territorial roads leading to the Santa Fe Trail, Shawnee also became the first county seat of Johnson County.

In 1862, Shawnee found itself in the middle of Civil War border struggles. The town was virtually destroyed, when it was burned and looted by southern guerillas led by William Quantrill just months before his infamous raid on Lawrence. After the County offices moved to Olathe in 1866, Shawnee became a small farm market center. During the 1950's, the population began to grow as people began moving away from congested urban areas to the smaller outlying towns. People quickly discovered the merits of the City and the population has continued to grow ever since, more than tripling in the last three decades.