The school was formerly known as Sekolah Menengah Agama Kota Kinabalu or SMAKK.

Establishment of this school was intended by the Sabah State Education Director in order to increase the number of Islamic schools in Sabah.

On 12 April 2011, SMKA Kota Kinabalu became a School Without Litter through a proclamation issued by Kota Kinabalu City Hall.

[2] In 2016, SMKA Kota Kinabalu becomes an SMKA with the status of Maahad Tahfiz (school of al-Quran memorisation) and, thus, offers Tahfiz programme to students.

Currently, the name of classes in the school is Bukhari, Muslim, Abu Daud, Tarmizi, An-Nasaie and Ibnu Majah (obsoleted).