He attended Nabumali High School in Mbale District and King's College Budo, in Wakiso District, both in Uganda. While at Kings College Budo (1959 to 1961), Aggrey was selected among a few others for elite military officers training at Sandhurst Military College in the United Kingdom. His father Canon Awori, however, rejected the idea of his talented son joining the military. From 1961 to 1965, he studied at Harvard University on a scholarship. The first year he took nuclear physics, but then switched over to political economics.