Inhabited in antiquity by the Creek, the land on which Auburn sits was opened to settlement in 1832 with the Treaty of Cusseta. The first settlers arrived in the winter of 1836 from Harris County, Georgia. These settlers, led by Judge John J. Harper, intended to build a town that would be the religious and educational center for the area. War soon broke out between treaty violators and the Creeks, which led to the Creeks being forcefully moved towards Oklahoma.
Auburn was incorporated on February 2, 1839, in what was then Macon County, covering an area of 2 square miles (5.2 km2). By that time, Methodist and Baptist churches had been established, and a school had been built and had come into operation. In the mid-1840s, separate academies for boys and girls were established in addition to the primary school. This concentration of educational institutions led to a rapid influx of families from the planter class into Auburn in the 1840s and 1850s. By 1858, of the roughly 1,000 free residents of Auburn, some 500 were students.
In 1856, the state legislature chartered a Methodist college, the East Alabama Male College in Auburn. This college, now Auburn University, opened its doors in 1859, offering a classical and liberal education.
With the advent of the Civil War in 1861, Auburn quickly emptied. All of the schools closed, and most businesses shuttered. Auburn was the site of a hospital for Texan Confederate soldiers, but only saw direct combat with the raids of Rousseau in 1864 and Wilson in 1865.