The present-day community of Brainerd sits on a well-drained, level plot of land, on the south side of gentle slope that rises up out of the valleys of Dry Creek, to the East, and the Whitewater River, to the West. The town is located in the northwest corner of Butler County, in Milton Township, about three miles southeast of Whitewater and the Harvey County Line.

Though Butler County was founded in 1855 as one of the state's original 33 counties, the first settler in the Brainerd area, Milton Snorf, did not stake out his claim until 1868, in the southeastern corner of what became Milton Township, far from the nearest towns of Towanda and Plum Grove. Over the next two decades of homesteading, land-clearing and home-building, a prosperous farm community emerged, centered on the township post office and schoolhouse at Holden, about a mile west of the future site of Brainerd.

In the mid-1870s, several Mennonite families arrived in the area from West Prussia, settling to the West and North of the present town site. One Prussian Mennonite, John Harder, purchased the tract of land in section 21, on the West side of what later became Broadway, Brainerd's Main Street. The arrival of additional Mennonite families from Prussia and Switzerland sparked the founding of a church, 2.5 miles north of town, on a site still occupied by the Emmaus Mennonite Church.

The land on which Brainerd grew up was first homesteaded in 1870, and was later owned by the land-speculating parents of that famous Kansas booster, Emporia Gazette editor William Allen White. Elisha B. Brainerd, a Civil War veteran from Pennsylvania, purchased the acreage in 1881. Four years later, a town was founded bearing his name, on property deeded by Brainerd and members of the Harder and Thierstein families to the Ellsworth, McPherson, Newton and Southeastern Railroad Company, which had decided to build a line between the Butler County seat of El Dorado and the Harvey County seat of Newton. The new line was slated to run through the center of Milton Township, and a station stop was planned for the new Brainerd town site.

The railroad finalized its purchase of the land parcels on April 21, 1885, and immediately set to work preparing the official survey of the town site. Long before the May 13 survey, 20 businesses had announced their intention of erecting buildings on the site, and lumber was hauled in to construct a lumberyard, hotel, livery stable, furniture store, feed store, drug store, general merchandise outlet, tin shop and bank. Carpenters milled about the town, in eager anticipation of the work to commence. One of these craftsmen was Levi Mellor, a journeyman carpenter who had come West from Ohio several years back and quickly found work in Towanda constructing schoolhouses, commercial buildings and homes for the fast-growing Butler County population.

Brainerd was officially founded on May 25, 1885. The first available lot was snatched up by Milton Snorf, the township's 1868 pioneer, who announced his plans to relocate from the once-expanding, now-dwindling nearby community of Plum Grove, to open on a general merchandise shop at the corner of Broadway and Neiman Street, kitty-corner to the new railroad station (on the south side of the railroad right-of-way, where the Brainerd Feed Store now stands). Snorf and the hordes of other merchants who followed were clearly anticipating a lucrative return on their investment in the soon-to-boom little railroad town.