The mosque's origin is attributed to the efforts of the influential Islamic scholar Sheikh Muhammad Abdulkarim Almaghili.

Almaghili, who was born in Tlemcen in present-day Algeria, taught for a while in Katsina when he visited the town in the late fifteenth century during the reign of Muhammadu Korau.

By the beginning of the 16th century, Katsina had become a very important commercial and academic center in Hausaland, and Gobarau mosque had grown into a famed institution of higher Islamic education.

A popular myth about the origin of Gobarau states that when Muhammadu Korau slew Jibda-Yaki Sanau, the last pagan king of Katsina, he desired to construct a mosque.

Muhammadu Korau consulted the Muslim scholars of that time, and they all agreed to a certain direction, except one Mallam Jodoma, who was a stranger.