The church is built on the edge of the site of the Roman city
Melite, which included all of
Mdina and a large part of present-day Rabat. There were numerous churches built on the site of the present church which dates from the 17th century. In 1336 bishop
Hilarius refers to the church as
ecclesia Sancti Pauli de crypta, and also mentions the cemetery and the Roman ditch. The present church was built to replace a church which was completed in 1578. The new church was built with funds provided by the noble woman
Guzmana Navarra on plans prepared by
Francesco Buonamici. Commenced in 1653, the church building was completed by
Lorenzo Gafà in 1683. Annexed with the church of St Paul is a smaller church dedicated to
St Publius which was rebuilt in 1692 and again in 1726 by Salvu Borg. The church was elevated to a
Minor Basilica in 2020. ==The grotto==