The Department of Indian Systems of Medicine functions under the Department of AYUSH Kerala, and is headed by the AYUSH Secretary. The Director of Indian Systems of Medicine, supported by 2 Joint Directors, one Administrative Officer, one Accounts Officer and Administrative Assistants control and administer the department at the state level. The department is head-quartered at the Directorate of Indian Systems of Medicine in the state capital Thiruvananthapuram. The district level administration is delegated to the District Medical Officers of the respective districts. All the Ayurveda, Yoga and Naturopathy, Unani and Siddha hospitals and dispensaries are administered by the Charge Medical Officers who function under the respective District Medical Officers. The Government Ayurveda Research Institute for Mental Diseases Kottakkal, Malappuram, Kerala Institute of Sports Ayurveda and Research, Thrissur also functions under the direct control of the Director of Indian Systems of Medicine.

Presently, as on date, 5,456 employees are working in the Department of Indian Systems of Medicine in various technical and supportive cadres with a committed vision of delivering comprehensive public health care through Indian Systems of Medicine to all sections of Kerala society.