APHCA is led by an Executive Committee, which comprises: the Chairperson; the Vice-Chairperson; three members elected by the country delegates annually from among themselves; and the immediate past Chairperson of the Commission.

The Senior Animal Production and Health Officer of the FAO Regional Office for Asia and the Pacific, based in Bangkok, is the Secretary of APHCA and the Executive Committee. The Executive Committee provides guidance and assistance in the timely implementation of programmes that have been approved by the Commission.

APHCA is mainly funded from annual membership fees paid by its member countries. These fees are fixed according to the country categories that are broadly related to Gross National Product. These fees are paid to the FAO Trust Fund. The Secretary and part of the APHCA Secretariat staff are provided by FAO.

 Furthermore, some countries established National Currency Funds (NCFs) to promote technical cooperation among developing member countries, these funds being available only for use in the country that provides them. The establishment of NCF was made a formal part of the Agreement for the Establishment of the Commission as a result of an amendment passed in 1979 at its 4th Annual Session. NFCs are administered by the members concerned.

Finally, APHCA is open to extra-budgetary contributions APHCA received first extra budget made by the Government of Australia A$175,000 during 1982-85 as special core budget support to the APHCA Trust Fund. These funds were used to support specific programmes on regional and national training courses, TCDC activities, foot-and-mouth disease (FMD) control, and rinderpest eradication in the region. APHCA members have continued to work with development partners to develop and prepare a programmes to support livestock production in the region.