Stanstead St Margaret is not mentioned in the Domesday Survey under its older name of Thele, and was probably (according to VCH) included in the manor of Hailey in Great Amwell. This was held by Geoffrey de Bech in 1086, and had passed to Ralph Pincerna by the early 12thc, from whom it was held by the Buruns. Aubrey de Vere, Earl of Oxford also appears to have had rights in the manor.
The nave of the church was built in the early 12thc. The church was made collegiate with 5 chaplains in 1316, when the chancel was remodelled and a N chapel and aisle were erected. The college was dissolved in 1431 and the aisle removed, but the arches of the N arcade are still visible on the exterior. The church was restored by the Rev. J. S. Pratt from c.1807, and this restoration inclued the addition of the W bell-cote. The N vestries were added in the later 19thc., and the church was restored again in 1903 for Septimius Croft of St Margaretsbury, Lord of the Manor.