Department of Indigenous Systems of Medicine enabled health delivery through our own Indigenous systems viz. Ayurveda, Siddha, Unani and Homeopathy. A separate department for Homoeopathy was started in the year 1972. Govt. Ayurveda Dispensaries, Hospitals and Colleges were functioning under one department till 1979 and as per GO(MS) No.115/1979/HD dated 21-06-1979, all Ayurveda Colleges were brought under a separate department and the Principal, Govt. Ayurveda College Thiruvananthapuram was appointed as the head of the department.

As per GO(RT) No. 2649/79/HD dated 20-09-1979, the department of Indigenous Systems of Medicine was renamed as department of Indian Systems of Medicine and Director, Indigenous Systems of Medicine to Director, Indian Systems of Medicine. In 2015, the department of Indian Systems of Medicine was brought under the newly formed department of AYUSH.