The church is built on part 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. The church building commenced in 1653 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.