It was built by Abd-al-Nabi Khan, governor of Mathura during the reign of Mughal Emperor Aurangzeb.

The Jama Masjid was commissioned in the period 1660-1661 by Abd-al-Nabi Khan, faujdar of Mathura under Aurangzeb.

[2] The ground which Abd-al-Nabi Khan selected as the site of his mosque was purchased from some butchas and the remainder, he obtained from a family of Kazis, whose descendants still occupy what is called Kusk Mahalla, one of the very few quarters of the city that are known by a Persian name.

When Saijid Bakir, their head quarreled with the local governor and made over all his rights to Chaubes, and others.

[citation needed] The Jama Masjid is located at the centre and highest point of Mathura, raised from the ground by a plinth.