Choudhury was born to a Bengali Muslim family in the village of Bagbari, near the town of Karimganj, then part of the Sylhet Sarkar of the Mughal Empire's Bengal Subah.
Khan was said to have given up his wealth to his younger brother, and become a da'i in Hindustan, taking with him a handwritten ancestral mus'haf by Mir Husayn (dating to 1056 AH / 1647 CE), gilded by Muhammad Yusuf Ali.
[3][4] Choudhury was among the seventeen families that had emigrated from Sylhet, with other families being that of Syed Bakht Majumdar of Sylhet town, the Mians of Sonatia, the ancestors of Principal Habibur Rahman and the ancestors of Khan Bahadur Mahmud Ali (former Assam minister).
[3][note 1] Modelled after the recently established Darul Uloom Deoband, it is considered to be the first true madrasa in the Greater Sylhet region, offering a standardised religious education in contrast to the informal institutions which had existed there previously.
[5] It 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.