Musa Khan Mosque is located on the western side of the Shahidullah Hall of Dhaka University, and is less than half a km to the south of the Khwaja Shahbaz’s Mosque. A high vaulted plinth with a three-domed mosque above and the grave of Musa Khan to its northeast comprise the mosque complex of Musa Khan. The whole complex was once enclosed by an outer wall, now completely gone.
The vaulted platform, 3.05m high, gives an outside measurement of 17.68m from north to south and 14.02m from east to west.
Underneath the platform there are a series of rooms, now badly damaged. In the eastern side are three independent rooms, each of which could be entered from the east by a single archway.
Each of these rooms is again divided into two halves by a wide north-south horizontal arch. Further beyond on the west are three independent rooms, each being connected with the eastern one by an archway. The southern most room in the eastern side has an additional opening on the southwestern corner, which leads to a narrow passage along the southern side underneath the platform.