The James Cook Historical Museum is housed in the former St Mary's Convent for the Sisters of Mercy, built in 1888-9.
Cooktown's economy was buoyant due to the town's role as a port for the region's mineral wealth, dominated by the Palmer River goldmines. The local Catholic Priest was appointed Bishop in 1887, and prioritised the establishment of the convent, day and boarding school for girls. Financed by his Irish relatives, the building was designed by former colonial architect FDG Stanley.
As gold production declined so did Cooktown. Businesses that were not prospering didn't rebuild after the destruction of the 1907 cyclone. St Mary's continued to operate until the 1930s. It was occupied by the US military during World War Two and then abandoned and earmarked for demolition.
The building was saved and donated to the National Trust for use as the James Cook Historical Museum. The grounds have been landscaped as the Joseph Banks Memorial Garden, planted with species identified by Banks and Dr Solander during their seven week stay at the Endeavour River in 1770. The museum holds many items related to the large Chinese population of Cooktown, including items from a temple formerly located on Charlotte Street.