It was the inspiration of the first Vicar Apostolic of Cooktown, Bishop John Hutchinson; designed by former colonial architect Francis Drummond Greville Stanley, of Brisbane; and staffed initially by Sisters of Mercy from Dunvargan in Ireland.

[2] Bishop Hutchinson was one of three Irish Augustinian Fathers who arrived in Cooktown in 1884 to take charge of the Pro-Vicariate of North Queensland, established in 1876 and extending from Cardwell to Cape York Peninsula.

In late 1887 Bishop Hutchinson returned to Ireland to recruit more priests and to encourage an order of sisters to establish a convent school at Cooktown.

There was an existing primary school, staffed by lay teachers, attached to St Mary's Pro-Cathedral in Cooktown, but Bishop Hutchinson envisaged a grander establishment which could offer a superior education, both religious and academic, to the girls (future wives and mothers) of Far North Queensland.

At the rear, the kitchen, scullery and servant's room formed a detached wing, connected to the main building via a covered way.

[2] The site selected was on the crest of the ridge running south from Grassy Hill, above the main street of Cooktown, with a spectacular view over the Endeavour River estuary.

[2] Bishop Hutchinson had made the establishment of the convent school at Cooktown a personal project, donating much of his own money and borrowing from his relatives in Ireland, but substantial funds were raised locally as well.

[2] Despite the decline of Cooktown - both in population and significance - St Mary's Convent and School remained an important educational facility for girls in far North Queensland until the 1930s.

St Mary's boarding school closed in the 1930s but co-educational day classes were continued until 1941,[4] when the building is understood to have been commandeered by United States military authorities.

[3] Following public protest, the building was donated to the National Trust of Queensland on condition that it be restored to house the collection of the James Cook Historical Museum at Cooktown.

[4] The new Museum was opened on 22 April 1970 by Her Majesty Queen Elizabeth II, during her visit to Australia to celebrate the bi-centenary of Cook's charting of the east coast.

[3] The former St Mary's Convent and School continues to be maintained by the National Trust, and is one of the principal tourist attractions in Cooktown.

The rear or eastern verandah is infilled but retains its original detailing of single columns cast-iron first-floor balustrade and deep vertical timbered valance at ground-floor level.

[2] The former single-storeyed hipped roof brick kitchen building remains to the rear on the north side; additions have been made adjacent to this to service the museum.

[2] On the western bay there are three centrally positioned long, narrow windows at ground-floor and first-floor levels, and above these a round vent with hood mould.

The former St Mary's Convent and School, erected 1888-89, is important in demonstrating the evolution of Queensland's history, in particular the dramatic rise and fall of Cooktown as a port, supply and administrative centre to the Palmer River goldfields in the last quarter of the 19th century.

Construction of the convent and school also demonstrates the importance attached by the colonising culture to establishing (religious) education, considered a "civilising" influence in remote districts of Queensland during the frontier phase of our history.

It is significant for its rarity value: few late 19th century buildings of this substance and decorative detail were erected in centres as remote as Cooktown, accessible only by sea in the 1880s.

Situated prominently on the ridge running south from Grassy Hill, the place is visible from the sea approach to the town, and has been considered a Cooktown landmark since its construction in the late 1880s.

The place has significant associations with the work of the Augustinian fathers, in particular Bishops Hutchinson and Murray, and the Sisters of Mercy, in the Vicariate Apostolic of Cooktown in the late 19th and early 20th centuries, and with the American military during the Second World War.