The mosque is composed of a five bay porch leading into a square central hall that is extended to the south by half a bay and four rooms flanking the central hall to the east and west. The porch is covered by domes that were rebuilt during the 1953 restoration. Its marble columns are crowned by capitals that are oval in section. Passing through the muqarnas portal, two steps lead into the domed central hall. The dome, 11.15 meters in diameter, is carried on pendentives. To the south, the mihrab is placed in a rectangular extension of the central hall raised by a step and covered by a semi-dome. This arrangement, used first in the original Fatih Mosque, was abandoned after the Atik Ali Pasa Mosque. (b. 1497)
The semi-dome at Rum Mehmed Pasa is carried on stalactite squinches that droop down to the corners of the walls, in tune with the six rows of stalactites crowning the mihrab. The women's prayer space, found on either side of the door upon entering, is doubled in area with wooden platforms that cross the entry with a narrow balcony. The side hospice (tabhane) rooms, equipped with a fireplace and shelving niches, open directly into the central hall and into each other. During the restoration, plaster was removed from the walls to reveal period decoration.
While the plan, the interior decoration, and to some extent the portico, are Ottoman in style, the mosque's exterior appearance is expressively Byzantine. Where most Ottoman mosques have used polygonal drums, the dome of Rum Mehmed Pasa Mosque sits on a circular drum, a common feature in Byzantine churches. Placed on a square base, its load is carried on arches on three sides and a semi-dome on the forth. These thick brick arches, complete with clerestory windows, culminate above the emergent roof creating a wavy effect along the cornice line. The arched frames of the drum windows, similarly, are extended beyond the skirts of the dome. These unusual domes are covered with lead in a manner typical of Ottoman mosques. The construction of the mosque is cut stone, with rows of brick introduced the base and drum of the dome. There is a single minaret on the northwest corner; stairs leading to its single balcony are accessed from outside the mosque.
Rum Mehmed Pasa was executed before the completion of his mosque and is buried in a separate tomb outside the western corner of the qibla wall. The tomb is an octagonal building made of ashlar stone and crowned by a dome without windows. The interior, with the single sarcophagus of the grand vizier, is lit by an upper and lower window on each side. His relatives are buried in the enclosed cemetery behind the mosque. Rum Mehmed Pasa patronized two other mosques, one in Bademiye (Aydin province) and the other in Tire (Izmir province), and a bedesten in Manisa.