EOTC-CFAO’s governance is structured in three tiers which consists of the General Assembly (GA), the Board of Management (BOM) and the General Manager (GM). The GA which is the ultimate decision making body of the organization comprises of some members of the Holy Synod of the EOC and individuals from different governmental and non-governmental organizations. On the other hand the GM is answerable to the BOM whose members are selected from among members of the GA.

Likewise, the EOTC-CFAO has a well established organizational structure which consists of Finance Service, Research and External Relation Service, Administration and Re-integration, Re-unification and institutional care (RRI) Service, and Community Development and Family Empowerment Department all of which are directly responsible to the General Manager. At a regional level we have Child Care Centers (CCCs) and Project Offices which are managed by program directors all of which are reporting to the Head Office in Addis Ababa. The GM who keeps an eye on the day–to-day activities of the organization is assisted by department and service heads as well as by support staff of the organization.