The foundation of this Authority go back to 2005 when the Malta Qualifications Council (MQC) was set up. MQC was remitted to oversee the development of the National Qualifications Framework in the context of lifelong learning and to work in partnership with learners, employers, as well as training and education providers to achieve and maintain excellence as a contribution towards the national effort for competitiveness.
In 2006, the National Commission for Higher Education (NCHE) was set up as a consultative and advisory body to government on the higher and further education sectors. NCHE contributed towards the development and launch of the Malta Government Scholarship Scheme, it drafted recommendations for a Further & Higher Education Strategy, and in 2010 published a Guide to Financial Support Schemes for Students in Further & Higher Education. The Commission for Further and Higher Education incorporated both the Malta Qualifications Council as well as the National Commission for Higher Education. In 2010, MQC was merged administratively with the NCHE and the two functioned as a single organization (NCHE-MQC) until the setting up of NCFHE in 2012.
In 2021, the National Commission for Further and Higher Education is being re-established as the Malta Further and Higher Education Authority (MFHEA), to seek to promote and develop further and higher education in Malta by means of regulation and by the promotion of best practices.