It was built in 1859 by Hugh Bradford as a private chapel for the former Jondaryan pastoral station, and the first service was held by preacher Benjamin Glennie late that year.

Stations at the time had small "village" communities for employees, there being a considerable number of people living on Jondaryan apart from the manager and his family.

[1] Churchgoing was important to the social structure of the community as well as spiritually and in 1859, James White is said to have arranged for an unknown Melbourne architect to provide a design for a church for Jondaryan.

It was constructed by an Irish carpenter called Hugh Bradford and used materials from Jondaryan and ordered in from Toowoomba.

The first service in the new church was conducted by the Reverend Benjamin Glennie, on 23 October 1859, an event recorded in his diary.

A Sunday school was also run by Mr White's wife, Anne, for children living on the station.

The pine pews and silky oak prayer book case were made by the Jondaryan station carpenter.

[1] In 1988-1890 reinforced concrete piers were introduced along the north and south walls to support steel beams inserted above the original timber stumps, which are no longer load bearing.

The building is on timber stumps and the roof is clad with corrugated iron and has a small belfry at the western end.

[1] St Annes Anglican Church, Jondaryan was listed on the Queensland Heritage Register on 21 October 1992 having satisfied the following criteria.

[1] The place has a special association with the life or work of a particular person, group or organisation of importance in Queensland's history.

It is also associated with the life and work of the Reverend Benjamin Glennie, the first incumbent Anglican clergyman on the Downs.