Prior to the building of St. Paul's, the medieval Parish Church of Honiton was St. Michael's, situated at the top of Church Hill, somewhat distant from the developing town. By the early 1830's it was felt that there was need for another church in the centre of the expanding community. Consequently the foundation stone of St. Paul's was laid on October 28th, 1835 and the building erected on the site of the old All Hallow's School chapel. This had been made available by the school whose buildings surrounded the new church. At Easter 1838 it was consecrated by Bishop Henry Philpotts of Exeter.

The church was built on a north/south axis and not east/west as usual. This is significant when considering the problems to be encountered by the second organ.