The MAFSC was established with the primary aim of training officers in order to meet the increasing demands of trained staff officers by the three Services. Prior to this formation, only a few officers were selected for such training at overseas staff colleges.

The establishment of MAFSC was first mooted in 1967 by the late YAB Tun Abdul Razak bin Dato' Hussein, who was then the Deputy Prime Minister and the Minister of Defence. Subsequently, the Armed Forces Council agreed to the formation of the College at its 123rd meeting on 27 October 1970.

"HAIGATE" was choosen as the temporary site for the College because of its colorful background, being and old but picturesque conglomeration of brick and wooden blocks of huts adjacent to the Ministry of Defence. The camp was first built during the post-war period and served as an Officers' Mess (Imphal Mess). It later became a series of temporary army camps, the last being Headquarters of Second Malaysian Infantry Division and Headquarters of Lines of Communication Engineer Regiment.

The College welcomed its first batch of 30 CP drawn from the three Services in January 1972. The intake was increased the following year when the College took in Officers from the Royal Malaysian Police and the Malaysian Civil Service in addition to those of the three Services, making a total of 32 CP.

In 1974, the College opened its door to Overseas Participants. Participants from friendly countries namely Australia, Indonesia, New Zealand, Thailand, and the United Kingdom joined the course. Since then, the CP intake has increased with a proportional representation of officers from overseas.

In its quest for quality and excellence, the College conducts a twinning programme with the University of Malaya for a Post Graduate Diploma in Strategic and Defence Studies. This programme for Staff College was initiated in 1995. The subjects for this diploma form part of the overall curriculum and they are conducted by the Faculty of Arts and Social Sciences, University of Malaya. A CP who successfully completes both will therefore be awarded two diplomas, that is the 'pass staff college' (psc) from MAFSC and a Post Graduate Diploma in Strategic and Defence Studies from the University of Malaya. Marks awarded for the Post Graduate Diploma in Strategic and Defence Studies are absorbed into the overall Staff College Course assessment. To implement this programme, the UM Programme Coordinator and six professors and lecturers are assigned to the College during the UM module.

In 2012, the College then switched the twinning programme with the National Defence University of Malaysia (NDUM) for a Executive Diploma in Strategic and Defence Studies (EDSDS). Future intention is to upgrade this Executive Diploma into Post Graduate Diploma by the year 2018.

Moving forward to become the centre of excellence for Defence Research and Studies, the College in the near future will occupied a purpose build facilities located in Putrajaya which will be known as PUSPAHANAS.