The native limestone guardhouse replaced an earlier wooden structure in 1872. It included a room for the non-commissioned officer of the guard, the guardroom, and the military prison, which included three solitary cells.
Most prisoners were enlisted men, held for disorderly conduct, insubordination, desertion, and even murder. Prisoners slept on straw bed sacks on the stone floor until 1881 when a "banquette" or platform was built. Soldiers on 24-hour guard duty looked after prisoners and tended to fort security.
Some of the original soldiers' carvings in the limestone blocks of the guardhouse are still visible, including the name of Sergeant Thomas Kenny, who was at Fort Hays for four years until it was abandoned in 1889. Kenny was a marksman and participated in military shooting competitions at Fort Leavenworth and Kansas City.