Prior to 1965, the institution existed as St. Mary School at the Base and was taken over as PAF Junior Model School in January 1965. It was upgraded to Secondary School in April 1969 and to the Higher Secondary Level in September 1982. The institution is affiliated with Federal Board of Intermediate & Secondary Education, Islamabad. The college has been re-designated as Fazaia Inter College Chaklala in February 2004.
Primarily Fazaia Intermediate College, Chaklala, caters for the educational requirements of the children of PAF personal serving at PAF Base Chaklala. However, available seats, if any, are also offered to the children of other serving personnel, retired PAF personnel, serving and retired Army / Navy personnel and civilians.