Department of Anatomy which is an integral and basic unit of any medical institute is as old as the college itself. The anatomy block was established by generous donations of the local Hindu philanthropists. Many illustrious professors who have been the architects of FJMC (now a constituent college of FJMU) headed this department. Prof. Dr. Basharat Yousaf (late) was a highly dedicated professional who laid down the foundation of the department on firm grounds and stream lined its smooth functioning.

Prof. Dr. Mussarat A.M. Khan proved to be an equally competent professor who further strengthened the department. Other professors who made their contribution are Prof. Dr. Tasneem Amer Raza, Prof. Dr. Rehana Azim, Prof. Dr. Iffat Badar, Prof. Dr. Tehreem Fatima,  Prof. Dr. Mamoona Naheed, Prof. Dr.Zahra Haider Bokhari,  and currently headed by Prof. Dr. Aliya Zahid. Under the supervision Prof. Dr. Iffat Badar in-service M.Phil. programme was started with four students, who are in the process of completion of their M.Phil. degree and are working on various research projects. The department is well-equipped with a histology laboratory, a dissection hall & museum and a large collection of preserved specimens and models to help improve the teaching standards.