Atkinson began with settlers from Gen. John O'Neill's second colonizing group in 1875, including Col. John Atkinson, but repeated flooding of the Elkhorn River forced the community to move to higher ground before it could take hold. A post office was established in 1876, followed by a general store; the town had 70 residents, a three-month school term in 1878, and Catholic Mass in private homes. Rail service became central to Atkinson's growth when the Sioux City and Pacific Railroad, renamed the Fremont Elkhorn and Missouri Valley Railroad in 1869 and completed in 1886, reached Atkinson in 1881 as Holt County gained rail links west to the Black Hills and east to the rest of the country. The railroad brought settlers, supplies, farm equipment, cattle, education, entertainment, and military movement, and increased business led to an official depot with living quarters for the station agent, William Bryant. Though some critics doubted the land's value, Atkinson eventually generated more rail business than O'Neill, and its farming expanded rapidly along the line later nicknamed the Cowboy Line. Later rail history in the area included orphan trains that placed children with families in Atkinson and nearby Stuart in 1912, a University of Nebraska traveling cow and hen exhibit that stopped in Atkinson in 1913, and the return of World War I soldiers in 1919.