Initially, the Ministry of Health and Family Welfare consisted of two departments, each led by a Secretary of the Government of India: the Department of Health and Family Welfare and the Department of Health Research. On August 7, 2014, through an extraordinary gazette notification, the Department of AIDS Control was merged with the Department of Health and Family Welfare and is now known as the National AIDS Control Organization (NACO).

The two departments of the Ministry are as follows:

Department of Health and Family Welfare

Department of Health Research

Ministry of Health and Family Welfare has the following two attached Offices :-

1. Directorate General of Health Services (DGHS): It is an attached office of the Department of Health and Family Welfare. DGHS provides technical advice on medical and public health matters and is involved in the implementation of various health services.

2. National Health Authority: It is responsible for the implementation of India's flagship public health insurance/assurance scheme "Ayushman Bharat - Pradhan Mantri Jan Arogya Yojana" and also handles the planning, technical framework, and implementation of the "National Digital Health Mission."