The Old Allen County Jail was built in 1869 and was in operation until 1958.  The original cells on the first floor were wooden with iron bars, but those cells were replaced in 1891 with the steel cage that is currently on the first floor of the jail.  That cage, state of the art for the time, held 16 total prisoners, four to each cell, while the front cell was used as a drunk tank, solitary confinement, or the women's cell, as the situation required.  The second floor of the jail contained living quarters for the jailer and his family.

In 1904, the county remodeled the jail and made cells in the upstairs area. The exterior stairway was removed and the door sealed. The second floor was divided into cells with steel doors and metal walls. There was a Women's Detention Cell and the room at the northwest was used as an office for the jailer or sheriff who also had a room or office in the Allen County Courthouse. With the opening of the new Allen County Courthouse and its modern jail facilities, the old county jail was finally closed in 1958.

A few dangerous criminals and hundreds of minor offenders were confined in the jail in the 89 years that the jail was open. More than a few prisoners escaped confinement from the jail over the years, many by removing the iron bars on the windows or by cutting a hole in the roof. Only a few months after the jail was opened, a small mob of men overpowered the sheriff and removed one E.G. Dalson from the jail on the evening of June 27, 1870. He was then taken to a barn outside of Iola, KS and hung. He had been jailed on charges of murdering his stepson. Despite this incident, two adjoining counties began sending their criminals to Allen County for incarceration in the jail during the later 1870s.  Many of the prisoners have left their mark on the jail, evidenced by the graffiti covering the walls of the first floor.  A few guests have even managed to find a relative's name scratched into the wall.

The Old Jail Museum is constructed with two-foot thick limestone walls and at one time the entire structure was covered with rough stucco.  The stucco was later removed except in the window recesses.  This was patchy and cracked, so all the remaining stucco was removed in the spring of 1986 when many window and plaster repairs were made.  The Old Jail Museum was used for several years to house all of the collections of the historical society that could not be placed in the Museum Room of the Courthouse. In 1977, the Old Jail was placed on the National Register of Historic Places by the U.S. Department of Interior.