The party that chose the site of Holton started at Milwaukee, Wisconsin, in May 1856. A train of six covered wagons, each drawn by two yoke of oxen, started the long trek to take Free State settlers to Kansas. They were financed by the Kansas Society of Milwaukee which was headed by E. D. Holton. They met General James H. Lane with two hundred men at Nebraska City, Nebraska, a rendezvous for Free State men. They followed the Jim Lane Road into Kansas approximately thirty miles. They came to Elk Creek, 2½ miles west of Holton, where they cut timbers to make a bridge, crossed it and made camp where Central School now stands. They liked the two streams (later named Banner Creek and Elk Creek) and the pleasant grassy hills, so they decided to stay. A company was organized and a civil engineer who was with them commenced the survey. They named the new town in honor of Mr. Holton, the Milwaukee abolitionist.
A log house 20 by 30 feet was erected; it was so planned that is could be used for a fort and was known as Jim Lane's Fort. In the spring of 1857, J. B. Ingerson surveyed the townsite lots.