The design of the church, in a postmodern-symbolic style, combines Baroque with elements of the architecture of Saint Peter's Basilica and Roman triumphal arches. It refers to buildings in Wadowice, Kraków and Rome, symbolising Karol Wojtyła's journey to the See of Peter. Construction began in 1984, the foundation stone was laid from the doors of Saint Peter's Basilica in the Vatican in 1988, and work was completed in 1991 with the consecration by Pope John Paul II. 
The church centrepiece is the main altar with a copy of Perugino's fresco from the Sistine Chapel. Two ribbons of red marble flow down from it, forming the outline of Saint Peter's Square with the site of the Pope's assassination, marked with red tiles on the floor. The red ribbons symbolise John Paul II’s  'trickles of blood' shed during the assassination attempt. A plaque with the date of the assassination – 13 May 1981 – was embedded in the main altar. In addition, there are two side altars– the Divine Mercy altar and the venerated Our Lady of Fatima altar. There are stained-glass windows referring to the apparitions of Fatima. 
Behind the church, a path modelled on the image of Golgotha was built on a hill in 2003. Stations of the Cross, tablets with the Decalogue and the Eight Beatitudes have been set up alongside it, and a Missionary Cross also stands on Golgotha. A statue of John Paul II, the work of Italian artist Luciano Minguzzi, was placed in front of the church. To the side is a chapel consecrated in 1986 by Cardinal Franciszek Macharski, and on the other side is a bell tower with three bells.