The organisation of the military tribunal system is very much in keeping with the Swiss militia system. The Armed Forces Attorney General stands at the head of the military tribunal system, but fulfils - in addition to his procedural duties - primarily administrative duties (supervision of procedure, basic and advanced training for members of the military tribunal system, etc.). Eight military tribunals of first instance, three military courts of appeal and - at the same level as the Swiss Federal Supreme Court - the Military Supreme Court observe the legal precedent that is handed down.

All the courts are headed by a president, who is normally a colonel in the military tribunal system. The military attorneys (prosecutors) hold the rank of lieutenant colonel or major, the examining magistrates are majors, captains or specialist officers and the clerks of court are normally specialist officers.