Iken was recorded in the 9th century as Icanho and in the 13th century as Ykene. One suggestion is that the original name meant "headland", another that it's a heel or spur of land belonging to Ica.

Along with nearby Sudbourne, Iken was evacuated during the Second World War so the area could be used for military training.

Historically, Iken was an important fishing village and had a number of trade routes; between 1780 and 1868, corn was transported from Iken Cliff to London. Much of the marshland was drained in the 19th century for farmland, but this was lost in 1953 (presumably during the great flood of that year) when the river broke through the banks between Iken and Snape.

The Anchorage, where the church stands, used to be an island; a branch of the river flowed south of it.