The direction of the Tohoku Medical Megabank Project falls under the jurisdiction of the Ministry of Education, Culture, Sports, Science, and Technology (MEXT). Studies in Iwate Prefecture are overseen by Iwate Medical University, while those in Miyagi Prefecture are overseen by Tohoku University.

Iwate Tohoku Medical Megabank consists of six divisions and an Executive Office. Iwate Tohoku Medical Megabank is implementing projects with the support of relevant organizations, such as the Iwate Prefectural and municipal governments and the Iwate Medical Association.

Organizational chart (current as of December 11, 2015)