The church is dedicated to Saints John and Paul who were martyred under Julian the Apostate's persecution in the 4th Century.
Below the church, there are 2nd and 3rd century Roman houses in which Christians worshipped, and according to tradition one of these houses belonged to the two martyrs in the 4th century. They were martyred on the night of January 26th/27th 361, and buried in secret in their house. This was not only a transgression against the edicts of Emperor Julian the Apostate, but also a violation of Roman burial laws. To prevent disease, all burials had to take place outside city walls. That they were buried here is a strong reminder of the important place relics have held and still hold in Catholic religious practice.
The first church here was built in the 4th century shortly after the deaths of the two martyrs, and remains of it can be seen in the present church, which was built in the medieval period. The first church was known as Titulus Bizantiis after Senator Byzantius. His son Pammachius built a basilica on the site, which was known as Titulus Pammachii and was one of the first parish churches in Rome. The synod listing from 499 uses this name. An inscription frome the 5th century names Pammachius as the founder. He was a personal friend of St Jerome, and after several years of public service, as a senator like his father had been, he gave his money to the poor and retired to a life of seclusion and prayer; undoubtedly a result of St Jerome's influence. The synod listing of 595 also mentions the church, but by this time it is known as SS. Johanis e Pauli.
The basilica was restored by Pope Leo I (440-461). In 1084, it was sacked by Norman raiders. Pope Paschal II (1099-1118) started restoring it, and this project was completed c. 1150 by Giovanni Cardinal Conti de Sutri. The church was restored and altered 1715-1718 under Fabrizio Cardinal Paolucci, in the late Baroque style. The remains of the saints' house was revealed in the 19th century.
It is served by Passionist fathers, who were installed here in the late 18th century.
In 1929, Eugenio Pacelli became the titular of this church. He was elected pope in 1939, taking the name Pius XII.
The last major restoration took place in the 20th century, when Francis Cardinal Spellman, titular of the church from 1946 to 1967, got financial support from Joseph Kennedy to restore the façade and to carry out new excavations. The current titular priest of the church is H.E. Edward Michael Cardinal Egan, Archbishop of New York, USA. He was appointed on February 21, 2001.
~From Churches of Rome