Although it is difficult to ascertain the exact date of construction of this masjid, oral traditions claim that it was first build by some soldiers during the Mughal occupation of town between 1665-1667. During their three years’ station here (Lachit Barphukan defeated the army in the battle of Itakhuli in 1667) the soldiers (among them Sayyid Firuz Khan Faujdar and Sayyid Salam Khan Mir Bakshi), must have felt the need for a place for offering prayers. And this need mighty have prompted them to set up a mosque. This theory gains ground since a grave of Mughal Emperor Aurangzeb’s second faujdar exists in the masjid till date.

In course of time the original masjid was destroyed, and in the 1850s it was rebuilt at its present site on a plot of land donated by a generous Muslim widow. Since it was located in the fringe of the town then, not many people visited it. Old Muslim residents preferred the Lakhtokia and Machkhowa masjids. But towards the beginning of the 20th century, the town began to expand and Muslim families started to settle in the former Company Bagan and Solabeel areas. The area came to be known as Hedayatpur and its residents began to throng the Bura Masjid. During the earthquake of 1897, the masjid was badly damaged and was rebuilt into a small Assam-type structure with brick foundation at the initiative of police officer Akhtar Hussain and contractor Ida Khan. Finally, in the 1980s, the mosque was reconstructed into the imposing RCC structure that we see today.