Before the station was opened North Head the site was used by the Aboriginal Communities and was known to be used as a special place for Koradgee healing and burial ceremonies. Some evidence can still be seen such as rock shelters and burial sites.The quaratine station came in use in 1828, and was used for nearly 150 years, it was used to quaritine travellers first by sea then then eventually by air, it was still seen as an important process to help keep disease away from the population of Australia. As well as travellers it was used at the turn of the century to isolate people after the outbreak of bubonic plague and by soldiers returning from World War I to prevent an outbreak of influenza. It was last used in the 1970's as emergency accomadation for people fleeing Cyclone Tracey. The building was clearly set out to keep different classes and races apart, as this was practiced all over Australia until after World War II. The buildings that have survived and the equipment and other artifacts are seen as a rare and important part of Australian History.

In 1984 The State and Federal Goverment Passed ownership on to the national parks and wildlife for it to be included in the Sydney Harbour National Park.

The quaratine station is known to be an extremely haunted place, which is not surprising with the diseases people suffered there and the amount of deaths connected with the area. Many ghosts have been witnessed and there have also been unexplainable lights, sudden temperature changes, visitors being tapped on their shoulder and/or their clothes being tugged.