The inscription on the episcopal throne states that this is the first church in Rome dedicated to Mary, mother of Jesus, although some claim that privilege belongs to the Basilica di Santa Maria Maggiore. It is certainly one of the oldest churches in the city. A Christian house-church was founded here about 220 by Pope Saint Callixtus I (217–222) on the site of the Taberna meritoria, a refuge for retired soldiers. The area was made available for Christian use by Emperor Alexander Severus when he settled a dispute between the Christians and tavern-keepers, saying, according to the Liber Pontificalis "I prefer that it should belong to those who honor God, whatever be their form of worship." In 340, when Pope Julius I (337–352) rebuilt the titulus Callixti on a larger scale, it became the titulus Iulii in commemoration of his patronage and one of the original 25 parishes in Rome.
The church underwent two restorations in the fifth and eighth centuries and in 1140-43 it was re-erected on its old foundations under Pope Innocent II. Innocent II razed the church along with the recently completed tomb of the Antipope Anacletus II, his former rival. Innocent II arranged for his own burial on the spot formerly occupied by the tomb.
The richly carved Ionic capitals reused along its nave were taken either from the ruins of the Baths of Caracalla or the nearby Temple of Isis on the Janiculum. When scholarship during the 19th century identified the faces in their carved decoration as Isis, Serapis and Harpocrates, a restoration under Pius IX in 1870 hammered off the offending faces.
The predecessor of the present church was probably built in the early fourth century and that church was itself the successor to one of the tituli, Early Christian basilicas ascribed to a patron and perhaps literally inscribed with his name. Although nothing remains to establish with certainty where any of the public Christian edifices of Rome before the time of Constantine the Great were situated, the basilica on this site was known as Titulus Callisti, based on a legend in the Liber Pontificalis, which ascribed the earliest church here to a foundation by Pope Callixtus I (died 222), whose remains, translated to the new structure, are preserved under the altar.
The inscriptions found in Santa Maria in Trastevere, a valuable resource illustrating the history of the Basilica, were collected and published by Vincenzo Forcella.