Tradition states that while living in Mecca, Choudhury was visited in a dream by the Islamic prophet Muhammad, who instructed him to return to his homeland and spread religious education.
The madrasa was established in Choudhury's own home, in the village of Bagbari near Karimganj, and was officially named in his honour.
It remained in this location for nearly a century, shifting to its present site in 1969 under the tenure of the then muhtamim (principal), Maulana Ashab Uddin.
[4][note 1] Over the course of its history, the Madinatul Uloom Bagbari came to play a very prominent role in producing Arabic language scholars in the Greater Sylhet region, a reputation it maintains to the present-day.
[3] The madrasa currently contains an Arabic epigraph from 1509 that denotes the construction of a mosque in Surjyadas village by Sher Malik, an officer of the Sultan of Bengal Alauddin Husain Shah.