The School of Foundations in Education ("SFE") was part of the new academic structure which came into effect at the Hong Kong Institute of Education ("HKIEd") from the 1998/99 academic year until September 2005, when HKIEd underwent another academic restructuring.

In line with the upgrading of HKIEd to a university-level institution and the development of Bachelor and Postgraduate programmes, a working group was set up by the Academic Board to recommend a new structure after wide consultation with all staff. On 5 June 1998, the Academic Board's recommendation to create four Schools and 12 Departments was endorsed by the Council for commencement in the 1998/99 academic year. Under this new structure, the four Schools were responsible for organising academic programmes, whereas the twelve Departments were reorganised within the four Schools and they could focus on extending their expertise in the different programmes and courses organised by their respective School and reported directly to the School Deans.

The SFE was responsible for organising all primary and special needs education programmes, including HKIEd's flagship Bachelor of Education in Primary programme, a Postgraduate Diploma in Education programme, and many in-service professional development courses. The SFE was committed to playing an active role in the advancement of teacher quality and professionalism in Hong Kong by integrating the teacher education experiences of the previous Colleges of Education with the latest research and best practice. The SFE also comprised the most number of Departments and Centres out of the four Schools. By July 2005, the SFE consisted of five Departments and four Centres. They included the Departments of Curriculum and Instruction; Educational Policy and Administration; Educational Psychology, Counselling and Learning Needs; Science; and Social Sciences; as well as the Centre for Citizenship Education, the Centre for Special Needs and Studies in Inclusive Education, the Humanities and Social Sciences Learning Centre, and the Professional Studies Learning Centre.

In 2004, after having successfully achieved self-accrediting university status, HKIEd decided to realign its organisational structure by merging the four Schools into two Faculties from September 2005: the Faculty of Languages, Arts and Sciences, and the Faculty of Professional and Early Childhood Education. Major academic and research developments were to be coordinated at the Institute level with implementation taking place at the Faculty and Department levels. The SFE and the other three Schools therefore ceased to exist from September 2005.