The first known reference to a priest at Cottingham is in the Chronicle of Meaux Abbey of the early 12th century, which records a priest here about 1150. The Domesday Book entry for Cottingham in 1086 records neither a church nor a priest but it is highly likely that both were present at this time.

The earliest part of the cruciform church, no doubt a development of an earlier church of which there is no part surviving in situ, is the nave, built after about 1320 in the Decorated style. The walls of the transepts and some of their detail are also of this time, but the transepts were probably completed later in the 14th century.

The present chancel was built when Nicholas de Luda was rector, from 1362 to 1383. He was appointed to the living by Edward Prince of Wales, known as the Black Prince, eldest son of King Edward III, who had married his cousin, the heiress Joan Wake, the Fair Maid of Kent, and lord of Cottingham manor. Their son reigned as King Richard II from 1377 to 1399. The chancel is an early example of the Perpendicular style.

Nicholas de Luda was a king's clerk. He held various appointments under King Edward III and a number of church appointments. He was a prebendary of Salisbury, St Asaph and Beverley.

The tower was probably completed about 1400 in the Perpendicular style. The pinnacles were added in 1744.

The interior owes much of its present appearance to restorations in the 19th and 20th centuries. However various earlier fittings survive, including a monumental brass to Nicholas de Luda, now in the north east corner of the sanctuary but formerly in various positions in the chancel.

Today St Mary's is Listed as a Grade One building. It stands as a monument to our faith in Jesus Christ, the Son of God, and the good news of God's kingdom.