According to ancient tradition, St. Apollinare was the first Bishop of Ravenna, consecrated and sent to evangelize the region by St. Peter himself.
The first church erected in his honor within Rome was built between the second half of the VII and beginning of the VIII century, during the full Byzantine domination. The first religious order to occupy the church were most likely Basilian monks who had fled to Rome because of the iconoclastic persecution. They are attributed with transferring martyrs in the underground of the primitive church. In 1284 there is evidence that a Chapter of Canons began living at the church, and remained there until 1576. The Basilica became a parish in 1562 and maintained this status until 1824.
From 1574 until 1773, the church was connected with the Germanic College (later the Germanic-Hungarian College), which had the adjacent Palace as its headquarters.The primitive Basilica was demolished and rebuilt by the initiative of Pope Benedict XIV, and designed by Ferdinando Fuga (1699-1782), also the architect of the Sacred Palaces. Today it is a typical example of the artistic transition from Baroque to Neo-Classical style.
In 1825 it was the seat of the Pontifical Roman Seminary.
In 1990 it became the Chapel of the Pontifical University of the Holy Cross.