The Equestrian Order is governed, as are all parts of the Church, by a formalized, hierarchal structure. At its head is the Sovereign Pontiff, represented by the cardinal, who serves unto death from the date of his appointment as Grand Master.

The Grand Master is followed in rank by the Grand Prior, who is now always the Latin Patriarch of Jerusalem, and by the Assessor of the Order, who holds the title of archbishop and who traditionally serves in another Curia post within the Vatican. The most senior layman of the Order holds the title Lieutenant General. The post is presently held by Prince Massimo-Lancellotti, who holds the rank Knight of the Collar. He is followed by the Governor General of the Order, who is presently Count Carduccl. Three vice governor generals follow in descending order, then the Chancellor, the Master of Ceremonies, and numerous members of the Grand Magistery, who tend to be appointed from large national jurisdictions from around the world.

Each nation has its own national jurisdiction, which is usually subdivided into smaller jurisdictions known as "Lleutenancies." Each Lieutenancy has a lieutenant who is elected or appointed by a senior Churchman of the area, usually one or more of the cardinals in the locality. The term is fixed. He is assisted by a governing council similar in structure to that of the Grand Magistery in Rome, allowing for local practice and custom to some extent. Investitures are held locally, although Grand Magistral investitures do take place annually as well.