The first mention of a church in Carnaby dates back to 1148 and 1153 when Robert de Percy granted the church to Bridlington Priory. In the 12th and 13th centuries it had two dependent chapels, one at Fraisthorpe and one in Auburn, but these later became separate curacies. A vicarage was ordained before 1268.
In 1521 there was a guild at Carnaby and in 1571 a guild house was included in a Crown grant and is believed to have still been standing as late as 1723. Two torches were left to the church in 1420 by Joan Mounceaux, who was the wife of the lord of Barmston Manor.
The Church of St John the Baptist is built mainly of stone with some flint and cobble, some parts have been rebuilt with brick. It consists of a chancel, nave, south aisle and west tower. Only the circular font has survived from the Norman Church. The earliest existing fabric, the south aisle, the aisle arcade and the tower arch are of 13th century date. It is believed there may have been a north aisle but this no longer exists. The present tower was built in the 15th century is of three stages, topped by an embattled parapet. The church was restored around 1680 and again in 1719.
In 1552 there were three bells up to 1968. Two bells were dated 1630 and the third 1693. The later bell was badly cracked but was restored in 1892.