It was officially established in 1862, but was used as a burial ground as early as 1844, and was one of the twelve original United States National Cemeteries designated by Abraham Lincoln.

Administered by the United States Department of Veterans Affairs, it occupies approximately 36.1 acres (14.6 ha) and was site to over 22,00 interments, as of 2020.

On July 17, 1862, Congress enacted legislation that authorized the purchase of cemetery grounds to be used "for soldiers who shall have died in the service of the country".

In addition, the cemetery was used as the burial ground for soldiers who served at frontier posts of New Mexico, Arizona, Colorado and Wyoming.

After the Indian Wars, between 1885 and 1907 many of the western Army outposts were vacated and as many as 2,000 remains were re-interred at Fort Leavenworth.