Leavenworth Penitentiary in eastern Kansas was the first of three federal prisons authorized during the 1890s to avoid housing federal prisoners in state prisons known for scandal and mistreatment of inmates. Prisoners have been incarcerated in the Leavenworth area since before Kansas gained statehood in 1861. At that time, a territorial jail there became the first state penitentiary. Congress established the U.S. Army Disciplinary Barracks at Fort Leavenworth in 1874. In 1895 Congress ordered the military prison transferred to the Department of Justice, creating one of the first federal prisons for civilian offenders. (The U.S. government operated a penitentiary in Washington DC from 1831 to 1862 as well as territorial prisons.)

During the next eleven years, inmates marched from the fort to a nearby construction site on the military reservation where they built the Leavenworth Penitentiary according to plans drawn by the St. Louis architecture firm Eames and Young. The lack of skilled labor and the painstaking security measures necessitated by using convict laborers made for slow progress. Inmates began occupying the new facility in 1903, but the population did not transfer entirely from the military prison until 1906. Construction continued, with cell blocks completed by 1919, shoe shops by 1926, a brush and broom factory by 1928, and the offices and rotunda by 1929. The penitentiary became a tourist attraction even as it was being built. The arrival of 200 tourists from Kansas City in a single day in 1910 led the warden to suspend tours temporarily. Planners expected 1,200 cells would accommodate 1,200 prisoners, but crowding led officials to abandon that ideal. As early as 1915 the prison population reached 1,800. By 1925 the population had climbed to 3,262. Continued crowding led to another annexation of the Fort Leavenworth Disciplinary Barracks from 1929 through 1940. At the beginning of the twenty-first century, the penitentiary housed 1,726 inmates.