The Kisauni Islamic Institute was established in 9th November 1980 with the assistance of Dar Al-Ifta of Saudi Arabia. The institute offers a High school (Thanawi) certificate in Islamic Religious education with the medium of instruction being Arabic. The duration of the course has been revised from 3 years to an intensive 2 years. The institute has been a hallmark of Islamic studies in the region admitting students from East Africa and as far as Somalia, Ethiopia, Madagascar and Comoro Island.

Since inception to date, over 2,028 persons have graduated from the institute with many continuing their academic journeys to become renowned Islamic scholars. After the lull occasioned by the Covid-19 pandemic, the institute has been revitalized and is on its way to regaining its hallowed status as the institution of choice for Islamic studies in Kenya, East Africa and the Horn Region.

The institute has secured sponsorship through the HIBA Foundation and its affairs are run by the Mombasa Committee headed by Dr. Farooqui and Dr. Harun. The student population is currently at 63 and expected to grow to over 100 at the start of 2024 pending new admissions. 

As part of its revamped image, there are plans to open a skills development center at the institute and this will be incorporated into the main syllabus so that the graduates acquire an additional artisan skill as part of their studies. The aim is to produce graduates with Islamic knowledge and who can be self- sufficient in their economic needs by practicing a skill.