The school used to be located in Klang (1982) and Petaling Jaya (1983–87), Selangor and named Sekolah Menengah Agama Wilayah Persekutuan, before it moved to Labu in 1987.

Following a demonstration by its students in the school compound in Klang as well as at Ministry's office at Lebuh Pasar Besar Kuala Lumpur (making front-page coverage by several print medias), after one year of temporary lodging at KIK (now known as KISAS), in January 1983 SMAWP was relocated to a temporary building in the campus of International Islamic University Malaysia (Universiti Islam Antarabangsa Malaysia), in Section 16, Petaling Jaya.

At the same time, the Ministry of Education (Malaysia) solved their problem in April 1987 by lending a building in KM 11, Jalan Labu which was supposed to be the place for a 'Maktab Perguruan'.

A year later, the school members, consisted of 73 teachers and 1000 students, led by the next principal, Tuan Hj Mahmud bin Mohd Rashid, successfully uplifted the school's status and resulted in SMAP being 'adopted' by the International Islamic University Malaysia (Universiti Islam Antarabangsa Malaysia) and Forestry Department (Jabatan Perhutanan).

During his time of service, in 1997, Dato' Seri Najib Tun Razak (then Minister of Education) came to the school to announce the SPM 1996 results himself.

In 2002, SMAP gained a three-storey building for the Biology laboratories, workshops for the Studies of Living Skills, Form 1 classes and the Islamic Art and Culture studio.

In 2005, SMAP gained another new building, a two-storey ICT lab, as a faculty to enhance student intellectual skills in computers and programming.

The current senior assistant of Students' Affairs is Tuan Haji Rojahan bin Abdullah, who used to serve at SM Agama Persekutuan Bentong (SUPERB).