The RCE is fed by the national EPI programmes, the national medicines procurement and supplies agencies, the Ministries of Health Policy and Planning units, and the national medical teaching universities. These form the Expert Working Group that supports the RCE.

Immediately above the RCE is the National Steering Committee (which doubles as the Board of Management, the composition of which is described in the organizational chart below). This feeds into the Regional Steering Committee (RSC) that is within the sphere of the EAC Secretariat. At this level is also the Partners Forum, which combines advisory and conduit roles to feed into the EAC Sectoral Council of Ministers of Health.

Above this level is the full Council of Ministers of EAC Affairs and finally, the Summit.

At national level, the RCE reports to the University of Rwanda College of Medicine and Health Sciences for academic programs and to the Vice Chancellor Office (VCO) for policy and programing.