The museum records the history of the serial escapee Moondyne Joe[1] and his imprisonment in the "native cell".

The new force was led by John Drummond, who had become friendly with the Noongar people and, with his Aboriginal troopers, made regular patrols around the district.

Samuel Pole Phillips was appointed as the local justice of the peace, to support the work of the resident magistrate.

After the murder of Chidlow and Jones by a group of 40 Aboriginals, Govorner Hutt, in 1837, ordered a substantial barracks and stables to be built on the Toodyay townsite on lot R1.

A new lockup to serve as a gaol was built on the Toodyay townsite on lot R66 in Charles Street.

In April 1851, the convict ship Pyrenees arrived,[3] which forced Governor Charles Fitzgerald to establish depots in country areas.

The accompanying Pensioner Guards, ex military, who had been offered land as an incentive to come to the colony, acted as a special police force for emergencies.

These were worked out on a plan of the town but were later cancelled when the Pensioner Guards were moved to the new depot site, which was two miles further upstream.

In 1860–61 it was decided to abandon the Toodyay townsite due to more floods in those years and the preceding ones, and to move to the centre of the depot site.

After World War II for nearly 20 years the building slowly deteriorated until a restoration programme was undertaken in 1962, and the museum began.

The displays have constantly improved over the years and now include the Moondyne Joe Gallery and the "Native" Cell.

The façade facing the street is solid stonework with five small high level openings.

[4]: 224–225  Restoration of the building began in the 1970s and the stables are currently open as part of the Old Gaol Museum complex.