Replacing temporary structures including prison hulks in the Bay of Port Phillip and holding yards in Ballarat, the gaol operated between 1862 and 1965.

This prison design carried on a revolution begun in 1829 by Eastern State Penitentiary in Philadelphia.

The principle of the design being that one guard would stand in the centre of the hall and at one glance survey all cells.

In 1862 a tunnel was constructed to join the gaol to the adjacent Ballarat Courthouse, allowing for the safe transfer of prisoners.

The old warden's residence is now home to the Australian Centre for Research into Injury in Sports and its Prevention (ACRISP).