Construction of the new parish church of Mission Basilica San Juan Capistrano, was completed in 1986. The church is designed after the Great Stone Church which was destroyed by the great earthquake of 1812. The ruins of the Great Stone Church are located on the Historic Mission grounds, which is open to tourists on a daily basis. 

With only a portion of the original Stone Church surviving, it was not possible to build a complete replica. Research on similar contemporaneous churches in California and Mexico supplied information for the missing elements. The walls of this church are two feet thick. Modern building materials and techniques were chosen so that the church would be built to withstand an earthquake.

The motifs on the interior walls were designed and painted by the artist, Dr. Norman Neuerberg. Dr. Neuerberg studied the Great Stone Church and visited the island of Mallorca, Spain, the homeland of Fr. Junipero Serra, founder of the Mission. It took Dr. Neuerberg eighteen months to complete all the interior wall paintings.

The first Mass in the new church was celebrated on October 23, 1986. Masses were offered prior to that on Christmas 1984 and Easter 1986 in the uncompleted church. On February 8, 1987, Cardinal Timothy Manning officially dedicated the church.

In the Jubilee Year of 2000, Pope John Paul II proclaimed the Mission Church of San Juan Capistrano a Basilica. This is a title of honor granted by the Holy See to churches that have achieved special religious, historical, and cultural significance. Churches granted this title carry a particular relationship with the Holy See. They are designated as places where the Holy Father and the Petrine ministry are honored and supported with special solemnity.

A church honored as a basilica becomes a special gathering place—a pilgrimage center—for the larger faith community and bears a special bond with the Holy See from which it received its title. The following Basilica symbols illustrate both this charge and this relationship:

Papal Crest

On the outside of the Mission Basilica, over the principal entrances, is the official coat of arms of the reigning pontiff, Pope Francis. The crest announces in symbol that pilgrims are entering a special place both honored by and dedicated to the Holy Father.

Tintinabellum (Basilica Bell)

On the right side of the sanctuary is a sliver bell characteristic of a Basilica. It is also a symbol of papacy and pilgrimage.

Ombrellino (Basilica Umbrella)

Inside the sanctuary, near the ambo (pulpit), is a Basilica ombrellino. It is reminiscent of the days long past when a processional umbrella protected the holy Father from the elements on his travels. 

On the Feast of St. Joseph, March 19, 2003, the U.S. National Conference of Catholic Bishops designated Mission San Juan Capistrano as a National Shrine. This high honor was in recognition of the Mission’s effective service to the spiritual, liturgical and devotional life of pilgrims from across the United States and the international community. As a National Shrine, Mission Basilica San Juan Capistrano is an officially sanctioned and recommended place of pilgrimage. It is dedicated to inspiring and fostering the deeper spiritual renewal sought by religious pilgrims.