From about 5000 BC until Uriah Stones navigated up an off-shoot of the Cumberland River in 1766, what is now Rutherford County was inhabited by Native Americans. The last tribes in Middle Tennessee were the Chickasaw, Cherokee and Creek Indians. They used the area as their hunting grounds. When white settlers began the westward movement into Tennessee from places like North Carolina, South Carolina and Virginia, the Native Americans were forced to find other areas to hunt and live. Most of these new Tennesseans held land grants from the Revolutionary War. They planted corn and built homes from logs. Lumber was shipped out of the area on flat boats up and down the river.

Rutherford County was formed in 1803 from parts of Davidson, Williamson and Wilson counties, and named in honor of Griffith Rutherford (1721-1805). Rutherford was a North Carolina colonial legislator and an American Revolutionary War general, who settled in Middle Tennessee after the Revolution. He was appointed President of the Council of the Southwest Territory (the upper chamber of the territorial legislature) in 1794.

The first county seat was established in the community of Jefferson, near Smyrna, and in 1811 the town of Cannonsburough was established as the new county seat. After just 33 days, the name of the town was changed to Murfreesborough, now Murfreesboro, in honor of Hardy Murfree, a Revolutionary War friend of William Lytle, who donated the land. In 1834 it was determined that the center of Tennessee was located on Old Lascassas Pike, one mile from downtown Murfreesboro. The location was nicknamed "the dimple of the universe" by local residents, and the spot was later marked with an obelisk by the Rutherford County Historical Society.

Rutherford County strongly supported the Confederacy during the Civil War, having voted 2,392 to 73 in favor of Tennessee's Ordinance of Secession on June 8, 1861. Rutherford County's central location and proximity to Nashville during the Civil War made it a contested area. The county was home to one of the bloodiest battles of the war, the Battle of Stones River, which was fought between December 31, 1861, and January 2, 1862. On July 13, 1862, Confederate General Nathan Bedford Forrest conducted a series of cavalry operations known locally as Forrest's Raid. The raid successfully led to the surrender of all Union forces occupying the area. Soon after his departure, Union troops returned to the area and held it until the end of the war.