There is reason to believe that at one time Flint (Welsh: Fflint) was a chapelry within the parish of Northop, but it has functioned as a separate parish for at least 400 years.
The earliest recorded reference to St. Mary's church dates from the thirteenth century. The original church was on the plan of a parallelogram. It had a north aisle, a porch, and a small wooden steeple at its west end. By 1846, the condition of the church had deteriorated so badly that it was considered to be unsafe, and permission was granted to worship in the Town Hall. The church was completely demolished and a new building, designed by the architect Ambrose Poynter, was erected on the same site. At the time, a number of old coffin lids and inscribed slabs were discovered in the foundations. The new church was consecrated on 5th December 1848.