The earliest record of a chapel at Ellel is in 1153, and until 1853 it was a chapel of ease for the church of St Michael in Cockerham.
The present church was consecrated in 1907, being a replacement for a chapel on a nearby site that was built in 1804. This was demolished in 1936.
The earliest registers for St John’s start in 1828. Prior to this they were included in the Cockerham registers.