The dean of Episcopal Divinity School at Union is the Rev. Dr. Kelly Brown Douglas, who assumed her post in September 2017. The Rev. Dr. William C. Nelsen, who has responsibility for EDS's transition in Cambridge, became interim president in September 2016. 

The school is governed by a Board of Trustees, which meets three times a year. The board’s Committee on Trustees (COT), oversees internal governance issues of the board, including the identification and nomination of new trustees.