The Ministry has several departments specializing in different aspects of health care. The department of Hospital Services is responsible for the building and renovation of health facilities in Ondo State. It is the department in charge of procurement and supply of health equipment to state owned health facilities.It is also responsible for the accreditation and supervision of all public and private health facilities operating or wishing to operate in Ondo State.

The department of Pharmaceutical Services is saddled with the responsibility of making drugs and dressings available for health care delivery in all public health Institutions in the state. It also touches on such other aspects as Pharmaceutical inspection and monitoring, eradication of counterfeit and fake and unwholesome drugs, closure of illegal Pharmaceutical premises, drug abuse control and Herbal research and development.

The department of Nursing Services is a professional supervisory department responsible for planning for effective and efficient nursing services and training in Ondo State. It also represents the Nursing and Midwifery Council of Nigeria in Ondo State through the Ondo State Nursing and Midwifery Committee. The department supervises the Schools of Nursing and Midwifery Council regulations.

The department of Planning, Research and Statistics is responsible for the planning and development of strategies for the effective implementation of the State Health policy and Plan. It is also responsible for the collection, collation, analysis, reporting and storage of Medical Statistics for the State. Within the purview of the department is the development of annual budgets for efficient performance of the Ministry, conduct of research studies on health activities in the State, monitoring of activities in respect of set targets, preparation of quarterly and yearly reports and identification of training needs.

Finance and Administration department services all the other departments of the Ministry. The department sees to the general welfare of staff of the Ministry, it undertakes the processes of appointment, promotion and discipline. It also takes care of the Ministry Registry and handles the account unit.