The National Institute of Integrative Medicine was formed from the Graduate School of Integrative Medicine (GSIM), formerly a part of Swinburne University in Melbourne, Victoria. GSIM was founded by Professor Avni Sali in 1997 as a reflection of the growing demand in the medical community to combine Complementary Medicine and Conventional medical practice.

As a development of GSIM, Professor Sali formed the NIIM as a Not-For-Profit organisation in 2005. With the generous support of a group of prominent Australians, a property in Hawthorn was purchased to house the NIM headquarters. With the help of volunteers and generous donations, the property was renovated to suit the purposes of research, education and practice of Integrative Medicine.

The Institute soon began initiating and supporting health research and awareness projects. In its first years as an independent institution, NIIM collaborated with organisations such as the University of Queensland in facilitating a short-course in Integrative Medicine for medical practitioners, and the Swinburne Brain Sciences Institute. Today, NIIM hosts, collaborates with and sponsors lecturers, doctors and leading academic minds in research and education, providing the community with an innovative medical facility equipped to recognise and implement the changes required in the expanding medical field.

In March 2009, the NIIM Wellness Clinic began operation, providing Integrative General Practice, Traditional Chinese Medicine and Osteopathy, with the addition of other modalities such as Naturopathy, Live Blood Analysis and Exercise Physiology shortly afterward. The Clinic continues to expand in the services available, offering screening and treatment options unique to the field of Integrative Medicine.