Before partition, Army Pathology services for Northern India were housed in a small laboratory in Rawalpindi named Command Laboratory Northern Command India. At the time of independence in 1947, it was converted into Central Military Pathology Laboratory to serve as the reference laboratory for the medical units of all three services. This unit was expanded and renamed Armed Forces Institute of Pathology (AFIP) Rawalpindi on 20th August 1957. This institute initially located in a double story building underwent progressive expansion over years to include Department of Nuclear Medicine in 1979 and Advanced Diagnostic and Research Centre in 1988.

Presently AFIP Rawalpindi provides standard diagnostic services to the Armed Forces personnel and civilian population. The institute has qualified technical staff to run high tech instruments and provides diagnostic services in Chemical Pathology, Endocrinology, Microbiology, Histopathology, Haematology, Virology, Immunology and Nuclear Medicine. It is also responsible for high quality diagnostic services. Institute ensures that all its diagnostic activities meet the requirements of ISO 15189:2007 and satisfies the needs of patients and clinical personnel responsible for patient care. There is a constant endeavour to improve the existing facilities and enhance the present list of available diagnostic facility. Forensic Medical Sciences Laboratory (FMSL) has been established in Oct 2012. FMSL houses state of the art equipment with an aim to provide forensic lab facility in the discipline of Forensic Toxicology, Forensic Pathology (Post mortems), Forensic DNA and Forensic Microbiology with the potential to incorporate other forensic facilities.