In July 1854, John W. Brown came to this area and found it highly suitable for a homestead. He acquired through bartering with local Indians. He built a large brick farmhouse and later returned home to Missouri to tell his family and friends about the area. Some returned with him. In 1856, Mr. Brown along with M. C. Dickey, Loring Farnsworth and Henry Fox pre-empted for the purpose of a town. They christened it Brownsville, although the name was changed in the 1860s due to the fact there was another city with the same name. This was before the introduction of postal codes. It was located on the California Road and work began at once on the many buildings needed in a town of Brownsville's size. Two daily stage lines brought mail and people to the town and business was very good.
Robert Simmerwell was a missionary to the Indians in Auburn. He originally served as a missionary among the Pottawatomie Indians in Michigan Territory, while he apprenticed to a blacksmith and attended school at night. He later came to the Baptist Shawnee Mission on Pottawatomie Creek in eastern Kansas. In 1848 the government set up a new mission a few miles west of Topeka. In a three-story stone building with twelve rooms, boys and girls were given instruction in the manual arts, as well as in reading, writing, arithmetic, and religious subjects. In the fall of 1854, he and his wife had retired from active work in the Pottawatomie Mission, to homestead on southwest of the town.
In the 1850s, the city grew fast, and was often referred to as a "boom town". It was one of the largest in the state, and nearly became the state capital. However, Auburn was cast aside as an option, as the railroad bypassed the city. Topeka was chosen to be the capital because it had the railroad and an important ferry site along the Kansas River. The population dwindled, but continued to hover around 100 for many decades.
A description of the town from a 1912 volume of Kansas: A Cyclopedia of State History is as follows:
Auburn, a money order post office of Shawnee county, is in the township of the same name, about southwest of Topeka and west of Wakarusa, which is the nearest railroad station. It is a trading center for that section of the county, has Baptist, Methodist and Presbyterian churches, telephone connection with Topeka and other adjacent points, and in 1910 reported a population of 72. Two rural free delivery routes start from the Auburn office and supply daily mail to the farmers of the vicinity.
Auburn finally began to grow in population in the 1950s. An important issue at this time was the city's small school system. It consisted of Auburn Grade School (grades K-5) and Auburn High School (grades 6-12). The Highschool was quickly becoming overcrowded, and in the late 1950s, a new building was built. However, it was eventually decided that the Auburn School district would merge with the Washburn School District to increase efficiency. The last class graduated from Auburn High in 1966. The high school became Auburn Middle School, and in the late 1980s closed and converted to a community center, and the grade school remains open to this day.
In the 1960s and 1970s, the city's population shrank, but was re-vitalized with a large housing project. Between 1975 and 1985, roughly 100 new split-level homes were built. Since then, many more have sprung up.
During the years of 2000-2006, a pasture on the northeast side of Auburn was developed. A retirement home and three small, two-story apartment complexes have been built, resulting in the creation of residence for around 100 people.
In October 2009, held its 100th annual Grange Fair, which originally was originally started as the Shawnee County Free Fair in 1909.
Currently, city Founder John W. Brown's historic farmhouse and the surrounding land sit 3/4 miles southwest of city limits on a gravel road. Research conducted by the state historical society states it may be the oldest standing building in Shawnee County. However, it is not an official historical site. The property is owned by a local family by the name of Kresie. The Kresies purchased it in 1918 from the farm's second owner, and currently, it is in size and produces row crops.
The city itself contains several businesses. There is a locally owned grocery store, a Phillips 66 gas station, a full-service Vicker's station, a law office, a dentist, a veterinary clinic, a chiropractor, a pizza parlor, a liquor store, a Dollar General (which opened in late 2009), and an upper-end used car dealership as well as others. Most Auburn residents commute to other surrounding cities for work, often Topeka. Currently, there are four churches in Auburn: Presbyterian, Christian, Methodist and Baptist. The Auburn Community Center houses a community library. Many people in Auburn also belong to groups such as the Kiwanis Club, the Boy Scout troop, the Baseball Association. There is also a currently inactive Masonic Lodge.
Auburn has four police officers, two patrol cars, and a fully equipped volunteer fire department. There is also a road maintenance and utilities department and several Civil Defense volunteers who live in the town.