The DRDO is headed by the Scientific Advisor to the Raksha Mantri (Defence Minister) who is also the Director General Research & Development in the Ministry of Defence and the Secretary, Department of Defence Research & Development (DDR&D). At the headquarters level, he is assisted by Chief Controller (s) Research & Development (CCR&D), Technical and Corporate Directorates. Corporate Directorates cover the area/function of Personnel, Finance & Resources, Training, Civil Works & Estates, Raj Bhasha, Vigilance & O&M, etc and Technical Directorates act as an interface between the Laboratories and the Chief Controllers and the Scientific Advisor to the RM. The Addl Financial Adviser advices the organisation on the proper utilisation of the finances as per the objectives of the organisation.

The various directorates in the Headquarters are as follows: