The history of the faculty, runs back to the late 90s, but in 2001, it was first established as the "MSc Section" of then Kotelawala Defence Academy (KDA), to offer the MSc (Defence Studies) Degree in Management for senior officers of the Tri-Services, Police, public and private sectors. With the high demand for the Master"s degree programme, the University introduced a BSc (Defence Studies) Degree in Management, for those who were considered as deserving middle-level officers in 2003. Thereafter, the "MSc Section" was renamed on several occasions: in 2004 as the Staff Development and Career Advancement Division, in 2007 as the Institute of Postgraduate Studies, and finally in 2012 as the Faculty of Graduate Studies (FGS). Since the inception, the Faculty has been served by several Deans of different calibers, and is of both military and civil. 

The FGS has been in the forefront by ensuring personal and professional growth of participants through interactive sessions, experimental learning, and independent research projects. The FGS has being responsible for the conduct of all postgraduate degree programmes at KDU for personnel in the Tri-Services, Police, and the Executive Officers of public and private sectors. The majority of its courses are conducted during weekends for the convenience of its students to enable them to follow courses without compromising their duties in respective services. Course components have been designed to facilitate and enhance knowledge, develop skills, transform attitudes and to experiment approaches in problem solving. Further, the FGS has been providing opportunities for candidates to establish links with local and international scientists via local and international institutes. Further, the postgraduate students of KDU have been provided with and encouraged, to publish their research work in Indexed journals, peer-reviewed journals and to communicate those in both local and international research conferences. Hosting the KDU-IRC is one such avenue.

In 2024, the FGS opened its arms for the international community, by commencing its first postgraduate programme for international students, which is a one year Master of Business Administration Degree Programme and is for the academic year 2024-2025. This one year MBA programme is a significant milestone in our commitment to providing a global education experience.