An important role of the KEK is to educate graduate students, who may opt for one of the two systems of education. One is the educational system at the Graduate University for Advanced Studies (SOKENDAI), where KEK is in charge of the School of High Energy Accelerator Science that comprises the departments of Accelerator Science, Materials Structure Science, and Particle and Nuclear Physics. The other is the educational course that trains graduate students from other universities as a part of the collaboration between KEK and universities across Japan.

Furthermore, because of the unique inter-university research facilities available at KEK, a considerable number of doctoral theses, based on the research carried out at KEK, have been written at other universities. To educate students and young researchers from universities, research institutes, and private companies, various open seminars related to accelerator science are also conducted in collaboration with researchers outside KEK. Through these activities, KEK contributes to training researchers and technical experts in various fields related to accelerator science.