The Office is headed by the Commissioner for Federal Judicial Affairs who is assisted by the Deputy Commissioner, responsible for financial, personnel, communications and information systems, administrative matters and language training; by the Executive Editor responsible for editing the Federal Courts Reports; by the Executive Director of the Canadian Judicial Council; by the Executive Director, Judicial Appointments and Legal Counsel that administers the sixteen Advisory Committees on Judicial Appointments; and, by the Director of International Cooperation.

The Deputy Commissioner is assisted by the Director of Finance and Administrative Services; by the Director of Compensation, Benefits and Human Resources; by the Director of Communications and Information Systems; and, by the Director of Judges' Language Training.