The overall objective of WAHO is, together with the other Community Institutions, to contribute to the attainment of the ideal of the creation of an Economic Union of West Africa, in accordance with Article 3 of the Revised ECOWAS Treaty.

Specifically, the main objectives of WAHO are those described in its founding protocol, namely: 

• Promote research into the major endemic diseases in the region and undertake activities aimed at controlling these diseases and their eradication;
• Promote the training of medical specialists and of paramedical personnel and where necessary support the training of future medical graduates ; 
• Collect and disseminate technical information, epidemiological and others related to health research and training in Member States; 
• Assist in the establishment of technical information centres in Member States; 
• Promote and harmonize the establishment of laboratories for the production of vaccines, medicines manufacturing and quality control in the region; 
• Encourage cooperation in the control and eradication of drug dependency and abuse in the region; 
• Promote exchange of personnel and health technologies among Member States; 
• Provide advice on all health related aspects of development projects to Member States; 
• Support the strengthening of health services and infrastructures of Member States; 
• Provide assistance to Member States to resolve health problems in the event of emergencies following natural disasters; 
• Collaborate with sub-regional, regional and international organizations to address health problems in the region; 
• Promote cooperation between scientists and professionals groups contributing to health development; 
• Propose conventions, agreements, regulations and recommendations on regional health issues and undertake tasks entrusted to the Organization in this regard.