The main Jinnah Medical & Dental College building has six floors, while the Basic Sciences building has five stories. The Dean's Office, Boardroom, Student Affairs and Administrative offices are located on the ground floor.

An air-conditioned Auditorium with a seating capacity of 300 is located on the first floor and is equipped with a multimedia system and a modern audio-visual system. Spread over several floors, there are a total of seven lecture halls and ten seminar rooms. All lecture halls are air-conditioned and equipped with multimedia facilities. Basic Sciences laboratories, Dissection Hall, faculty offices and museums are located on the Ground, Third and Fourth floors.

The JMDC Dental Hospital is located on the second floor and consists of outpatient clinics, Dental Laboratories, Dental Museum and Dental faculty offices. The following departments provide quality treatment for a nominal registration fee:: Oral Surgery, Operative Dentistry, Periodontics, Prosthodontics and Orthodontics.
The previously named Medicare Hospital building is a seven floor building which is now being reconstructed into a modern complex for the development new facilities. Pharmacy department laboratories, museum and faculty offices are located on the third floor. The main JMDC Library is on the ground floor. Accounts and IT Departments are on the fourth floor. Eventually, a fully equipped Research Laboratory with Animal House will be part of this building.