Atchison County was named for David Rice Atchison, a Major General of the Missouri State Militia. The actual organization of Atchison County occurred in February, 1845 at the home of Conrad Cloepfil, with Alexander McElroy, David Hunsaker and Elijah Needles acting in the authorized capacity of commissioners of the county court. The officers of the court were appointed as the first step; McElroy as President, A. A. Bradford as clerk and Lite T. Tate as sheriff. They divided the county into 5 Townships: Clark, Polk, Tarkio, Nishnabotna and Bluff. It should be noted that Tarkio, Bluff and Polk Townships had over one half of their land in what later became the State of Iowa. This area was lost when the U.S. Supreme Court established the boundary line.

Atchison County, during the 1800's, was in the middle of a great period of expansion of the west. The Missouri River, known as the "Big Muddy", provided access and transportation across the Great Plains. It was used by the Indians and trappers and later by Lewis and Clark in their 1804 expedition. The U S Government established Forts in the area because of troubles with the Indians. Military supply roads connected these to the burgeoning east. These roads were heavily used by the westward bound wagon trains.

The first officially listed settler in the area was Major Stephen Cooper who arrived in the spring of 1836 with a permit from the Governor to carry on farming for the Pottawatamie Indians. He was located about 4 miles south of what is now Sidney, Iowa.

Also at the time there was a "French Colony" on the Nishnabotna River. Their settlement extended well into present-day Iowa from about two miles south of the state line.

In 1839 Hank Roberts and Thomas Wilson built sod houses near the town of Sonora. They were followed by Callaway Millsaps, Charles Beauchamp, Archibald and Alexander Handley.

In the 1840s, Charles Fanning built a grist mill in the Tarkio area. He planted some trees that are still standing in the South City Park.