During Auburn Prison's early years, visitors from across America and Europe came to see the prison. The price of admission was 12 1/2 cents until 1822 when it doubled to discourage visitors. An average yearly income from the visitor fee totaled $1,524. At the time this was enough to pay the salaries of the deputy keeper ($450), a clerk ($450), a turnkey ($350), a chaplain ($125), and a surgeon ($200).

The "Auburn system" evolved during the 1800s with a plan for inmates to work silently together during the day and return at night to individual calls. The plan included the striped suit, close cropped hair, lockstep, and harsh punishments, which included beatings and floggings.

In 1913 Thomas Mott Osborne was appointed chairman of a commission on prison reform. Osborne, under the guise of "Tom Brown," secretly entered the prison as a convict in order to gain a prisoner's perception of incarceration. From these experiences and other observations, the Mutual Welfare League was formed to allow prisoners a voice in prison affairs. It was a governing body of prisoners and was one of the first attempts at reformation rather than retribution.

Riots in 1929 and other ensuing problems led to modernization of the prison. By the 1950s, Auburn Prison had rebuilt and improved inmate life.