EACCR has its secretariat at Uganda Virus Research institute (UVRI), which is located in Entebbe, Uganda. The secretariat provides administrative and technical support to the 4 regional coordinating nodes for training (Kilimanjaro Christian Medical Centre-KCMC in Moshi, Tanzania), malaria (KEMRI-Wellcome Trust Research Programme in Kilifi, Kenya), tuberculosis (NIMR-Muhimbili in Dar es salaam, Tanzania) and HIV (UVRI in Uganda).

Prof. Kaleebu oversees the activities of the secretariat and the entire network. He chairs the Project Implementation Committee (PIC) which holds teleconferences every quarter.