The Australian Defence Force (ADF) had its first encounter with malaria at Gallipoli in 1915 although only with a few cases. By the end of WW1 the ADF had experienced the true impact of malaria with half of the Desert Mounted Corps in Palestine incapacitated by malaria and over 100 deaths.

At the beginning of the Pacific campaign of WWII there was a critical shortage of quinine in Australia. 90% of the worlds supply was produced in Indonesia which lay directly in the path of the advancing Japanese forces.

The Australian Army, under the guidance of Colonel N.H. Fairley, established a malaria experimental group in Cairns in 1943 where malaria was still present. With the assistance of Australian Malaria Control Units and Mobile Entomological Sections, the experimental group were able to advance their studies with sulphamerazine and atebrin. The final experiments in by the Cairns experimental group were conducted in March 1946.

During the Second World War, ADFMIDI (then known as Land HQ Medical Research Unit) conducted critically important drug trials in Cairns to determine the cause of malaria casualties in New Guinea and how best to use the limited medications available to protect soldiers during jungle warfare. This requirement continued into the Vietnam War when drug combinations were tested during actual combat operations and through more recent deployments in Timor-Leste.

The 1 Malaria Research Laboratory was established in 1967 by the efforts of R.H. Black, professor of Tropical Medicine at the School of Public Health and Tropical Medicine at Sydney University. Professor Black was also a consultant in tropical medicine to the ADF. Following the malaria problems experienced by troops in Vietnam, Black recommended research into malaria to minimise future problems with the disease.

The 1 Malarial Research Laboratory was originally located within the School of Public Health and Tropical Medicine. In 1973, it moved to the Ingleburn Army Camp and the name was changed to the Army Malaria Research Unit.

In 1996 the unit moved to a modern laboratory complex at Gallipoli Barracks, Brisbane and renamed the Australian Army Malaria Institute.

In 2017 the Army Malaria Institute was renamed the Australian Defence Force Malaria and Infectious Diseases Institute.