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The Master of Screen and Media Production is offered by the College of Humanities, Arts and Social Sciences over two years of full time study, or part-time equivalent. The course articulates with the Graduate Certificate in Screen and Media Production and the Graduate Diploma in Screen and Media Production.

The Master of Science (Water Resources Management) is a 72-unit program offered by the College of Science and Engineering.The course articulates with the Graduate Certificate in Science (Water Resources Management) and the Graduate Diploma in Science (Water Resources Management), and the sequentially developed topics allow progression through the three awards. Candidates who have completed either of these courses are awarded credit for related topics.

The Master of Science (Health Administration) is a 72-unit program involving coursework and a thesis which is offered by the College of Business, Government and Law.

The Master of Science (Groundwater Hydrology) is a 72-unit program offered by the College of Science and Engineering.The course articulates with the Graduate Certificate in Science (Groundwater Hydrology) and the Graduate Diploma in Science (Groundwater Hydrology) , and the sequentially developed topics allow progression through the three awards. Candidates who have completed either of these courses are awarded credit for related topics.

The Master of Science (Aquaculture) is a 72-unit program comprising coursework and industrial work placement offered by the College of Science and Engineering. The course articulates the 18-unit Graduate Certificate in Science (Aquaculture) and the 36-unit Graduate Diploma in Science (Aquaculture), and the sequentially developed topics allow progression through the three awards.

The Master of Science is a 72-unit program offered by the College of Science and Engineering. The Master of Science has specialisations in Chemistry, Computer Science, Mathematics, and Physics. There is a 54-unit pathway for students with a Bachelor degree in the same discipline as their specialisation.

The Master of Remote and Indigenous Health is a 54-unit program which is offered by the College of Medicine and Public Health through the Centre for Remote Health in Alice Springs. The course articulates with the Graduate Certificate in Remote Health Practice and the Graduate Diploma in Remote Health Practice and the sequentially developed topics allow progression through the three awards. The program was developed in collaboration with the Council of Remote Area Nurses of Australia (now CRANA Plus) building on work with the National Aboriginal Community Controlled Health Organisation (NACCHO), the services for Australian Rural and Remote Allied health (SARRAH) and the Australian College of Rural and Remote Medicine (ACRRM). It is offered on an external basis through Flinders Learning Online and residential intensives. Students who hold the graduate certificate or the graduate diploma are granted credit for topics already taken.

The Master of Physiotherapy is a 72-unit coursework program which is offered by the College of Nursing and Health Sciences. It requires two years of full time study and is not offered externally or on a part-time basis.The course equips graduates to meet the entry level competency standards specified by the Australian professional accrediting body, the Australian Physiotherapy Council.

The Master of Psychology (Clinical) is a 72-unit program offered by the College of Education, Psychology and Social Work.

The Master of Professional Psychology is a 36-unit program offered by the College of Education, Psychology and Social Work.