Aghdam Juma Mosque was built by architect Karbalayi Safikhan Garabaghi in the years 1868-1870. The core of the prayer hall project comprises traditional square shape bearing four pillars in the middle. Three rows of deep niches carved in the east and west sides of the square widened the space of the hall and gave it a rectangular shape. There is a high sanctuary niche in the middle of the south wall of the prayer hall. Elegant sanctuary niche bears an inscription of the name of the master of architectural décor (late Karbalayi Naggash Tabrizi’s son – master Mahammad Naggash Tabrizi) and repair date (1331 Hegira calendar, 1913 AD).

Proceeding with the tradition of Juma Mosques with two minarets widespread in medieval Azerbaijani architecture, architect Karbalayi Safikhan Garabaghi created the original type of mosque - Aghdam Juma Mosque in accordance with the call of his times, also architecture and construction experience of Karabakh.

In July, 1993, like other buildings, Juma Mosque was also demolished during the occupation of Aghdam. On November 20, 2020, Aghdam Juma Mosque was liberated from occupation.