The supreme authority of the Foundation is governed by Cracow's Metropolitan Archbishop Most Rev. Card. Stanisław Dziwisz. The Chairman of the Administrative Council is Most Rev. Card. Stanisław Ryłko.

The Administrative Secretariat of the Foundation is led by Rev. Dr. Krzysztof Wieliczko. The Secretariat provides support with respect to the activities of The Center for Documentation and Research of the Pontificate of John Paul II, as well as other institutions of the Foundation, such as: John Paul II Foundation - Casa per Ferie (Director: Msgr. Mieczyslaw Niepsuj) and John Paul II Foundation Home in Lublin (Director: Rev. Ryszard Krupa, SCJ).

The Center for Documentation and Research of the Pontificate of John Paul II is subdivided into the Documentation Division led by Rev. Antoni Pyznar, and the Research Division led by Rev. Dr. Andrzej Dobrzyński.

The Administrative Secretariat makes the Foundation present wherever possible and promotes the purposes of the Foundation. It also edits the quarterly Bulletin, which informs its readers about the work and activities of the Foundation.

The generous contributions of many benefactors from Poland and from all over the world make the work of the Foundation possible. Many of the benefactors are members in the Chapters and Societies of "Friends of the Foundation". There are 44 groups of Friends of the Foundation in 16 countries on four continents.