Built in 1863, Fort McPherson was established to ensure peace along the western frontier between the immigrants traveling along the Oregon Trail and the Native American inhabitants. The troops originally stationed at the post provided military protection from hostile Native Americans during the construction of the railroad.
To meet the burial needs of the soldiers stationed at the post, a cemetery was established early in its history. The old post burial ground was later moved to southwest of the post and some 50 remains were moved to this location.
Establishment of the 20-acre Fort McPherson National Cemetery in 1873 afforded the space to relocate remains from the cemeteries abandoned when the number of settlers decreased. Burial records testify that life on the frontier was full of hardships and dangers similar to battlefield camps during times of war.
The cemetery lodge was built in 1876 and rehabilitated in 1951 and 2000. About one mile southeast of the cemetery a monument marks the site of the flagstaff of the old military post. Another monument marks the route used by the Pony Express over the Oregon Trail, which passes through the cemetery.
The cemetery was listed on the National Register of Historic Places on May 5, 2012.