The original residence was built from 1870 to 1871 on a natural plateau overlooking Port Darwin. Locally quarried porcellanite stone was used in its construction with the lime for the mortar made from coral, and the original roof being made of coated canvas.
The first Government Resident, Captain William Bloomfield Douglas, supervised the addition of a verandah roofed with bark and other rooms made of timber. The second Government Resident, Mr George Byng Scott, added a second storey to the Residence, but this was rendered unsafe by termites and was removed by his successor, Mr Edward William Price.
Extensive renovations conducted from 1878 to 1879 by Government Secretary and architect, John George Knight, later to become the Government Resident (1890-1892), gave the building the shape it has today. Dr John Anderson Gilruth, upon his appointment as the first Administrator of the Northern Territory on 25 March 1912, changed the name from the 'Residence' to 'Government House'.
Government House was entered on the Register of the National Estate in 1980 and was declared a Place of Heritage under the Heritage Conservation Act on 15 March 1996.