In 1502, he was consecrated Bishop of London and became Keeper of the Great Seal, but his tenure of both offices was short, as in 1504, he became Lord Chancellor and Archbishop of Canterbury.

He resigned the office of Lord Chancellor in 1515 and was succeeded by Thomas Wolsey, whom he had consecrated as bishop of Lincoln in the previous year.

Warham was present at the Field of the Cloth of Gold in 1520 and assisted Wolsey as assessor during the secret inquiry into the validity of Henry's marriage with Catherine in 1527.

He was named as one of the counsellors to assist the queen, but, fearing to incur the king's displeasure and using his favourite phrase ira principis mors est ("the king's anger is death"), he gave her very little help and signed the letter to Pope Clement VII that urged the pope to assent to Henry's wish.

Warham presided over the Convocation of 1531, when the clergy of the Province of Canterbury voted £100,000 to the king to avoid the penalties of praemunire and accepted Henry as supreme head of the church with the face-saving clause "so far as the Law of Christ allows".

Having been munificent in his public and moderate in his private life, he died on a visit to his nephew, also William Warham.