Prior to the Reformation, there was a medieval church, which dated from at least the 15th century. Some claim that this church may have dated from the 12th century. It was dedicated to St John the Baptist. During the Reformation, St John's became the property of Edmund Sexton. This church was demolished in 1852 and was replaced by St John's Church of Ireland church. The old St John's cemetery is still there and contains a number of large tombs. This Protestant church is now closed and is under the ownership of Limerick Corporation.
St John's Roman Catholic parish had a church at Gallow's Green, which was outside the walls of the city in 1703. This was the first post-Reformation Roman Catholic in the parish of St John's and was built by Fr Jasper White P.P.
In 1730 a new church for the Roman Catholics of the parish was built on the site of the car park of the present Cathedral, near St John's Gate. Fr Denis O'Connor was the parish priest when the church was built.
In 1734, the parish priest Fr John Leahy took full control of the parish. It was formerly under the control of the Canon Regular of St Augustine. By 1753 the church from 1730 was falling into a dilapidated state and a simple church was built to replace it. This new church became the Pro-Cathedral and the parochial church until the construction of the Cathedral.
This church was more of a mass house than a church, as we know it today because it consisted of two or three small houses that were merged together. The parishes of St Michael and St John used the church. Fr John Leahy opened this new mass house in the parish of St John's. Fr Leahy is buried in St John's cemetery.
It is believed that this church was similar to St John's church in Cratloe, Co. Clare. This church of St John's was demolished after the completion of the Cathedral in 1861.