In the 3rd century, during the dynasty of the Severan emperors, the area where the basilica stands was part of an imperial villa called Horti Variani ad Spem Veterem, which included the Castrense Amphitheater, the Varian Circus, and the Helenian Baths (so named after their restoration by Empress Helena).

In 324, when Constantine moved the capital of the empire to Constantinople, the residence remained the property of his mother Helena, who had a chapel built inside the residence to preserve the relics of the Passion of Jesus. Christ, which she herself brought back to Rome after a trip to Jerusalem in 325. This chapel later became the original nucleus of the current Basilica of Santa Croce, which was originally called the "Eleniana Basilica."

The church underwent several renovations over the centuries. The foundation of a monastery in Santa Croce dates back to the 10th century, as attested by the funerary inscription of Benedict VII located next to the main entrance to the basilica.
During the pontificate of Pope Lucius II, in the 12th century, the church was transformed into the medieval style we still find today with its three-nave layout, with the addition of a Romanesque bell tower.

In February 1492, during the restoration of a mosaic, a box was discovered walled up in the apse arch of the church containing a walnut tablet kept inside a lead case with the three seals of Cardinal Gerardo Caccianemici, the future Pope Lucius II (1144-1145). The relic bears an inscription in three languages—Hebrew, Greek, and Latin—and is the Titulus Crucis: "Iesus Nazarenus Rex Iudaeorum", "Jesusù Nazarene king of the Jews", which we also know by the acronym I.N.R.I.

The basilica's current appearance is due to the renovation carried out by order of Benedict XIV between 1740 and 1758 by architects Pietro Passalacqua (1690-1748) and Domenico Gregorini (1692-1777), who permanently modified the church's façade in the late Baroque style. The façade is divided into three bays, the central one convex and the lateral ones concave. At the top, in the central section, are the statues of the Apostles: Constantine on the right and Helena on the left, with two angels adoring the Cross in the center.

Until 1930, the relics were kept in the underground chapel of Saint Helena; Today, however, they are located in a chapel in the left nave, designed by Florestano Di Fausto and accessible since 1930.
The Chapel of the Relics, also known as the Sanctuary of the Cross, houses three fragments of the Cross of Jesus Christ, found, according to tradition, by Saint Helena on Mount Calvary in Jerusalem, the Titulus Crucis discovered in 1492 in the apse of the basilica, and other relics of lesser importance added in subsequent years.

The interior of the basilica is the result of renovations and restructuring over the centuries, which are reflected in the medieval layout and Baroque decorations. The three naves are separated by eight ancient granite columns and six pilasters, four of which incorporate as many original columns built in the eighteenth century.
The frescoes in the apse are attributed to Antoniazzo Romano and Marco Palmezzano and are striking for their intense blue and gold. The pictorial cycle illustrates the events surrounding the discovery of the relics by the empress.

Some works by Corrado Giaquinto date back to the 18th century: on the ceiling of the central nave is the canvas of the Madonna presenting Saints Helen and Constantine to the Trinity (1744), on the vault of the presbytery is the canvas of the Apparition of the Cross, and on the wall of the apse are the frescoes of Moses making water spring from the rock and Moses and the bronze serpent.

Attached to the monastery of Santa Croce and nestled between the Aurelian Walls and the church, there is The ancient Castrense Amphitheater, built in the 3rd century and used as a garden for the basilica and the convent.
Behind the basilica, you can admire the remains of the Circus Varianus, where gladiatorial games and chariot races were held.