The church was constructed out of wood in a cruciform shape as a Clas, though it was damaged during Owain Glyndŵr's rebellion and the nave was rebuilt in stone.

[1] During the English Civil War, Oliver Cromwell's Roundheads used the church as a barracks and the south door for target practice with muskets.

It was also shot at by Royalist forces sieging the church; the door is still in use and still retains the bullet holes.

The referendum results for 17 of the 19 parishes were published in the House of Commons, all in favour of remaining part of the Church of England.

A second poll was therefore held in 1916; Llansilin voted to join the Church in Wales by 255–228, becoming the only parish in the referendums to do so.