In 1668 he was admitted archdeacon of Canterbury upon the king's presentation, but he resigned the post in 1670. In 1677, being now prolocutor of the Convocation, he was unexpectedly advanced to the archbishopric of Canterbury. He attended Charles II upon his deathbed, and "made to him a very weighty exhortation, in which he used a good degree of freedom." He crowned King James II in 1685. Sancroft wrote with his own hand the petition presented in 1687 against the reading of the Declaration of Indulgence, which was signed by himself and six of his suffragans (collectively known as the Seven Bishops). For this they were all committed to the Tower of London, but were acquitted.
Many years after it was composed, John Overall's Convocation Book was published by Sancroft, to justify the principles of his Nonjuring party. The book was “on the subject of Government, the divine institution of which was very positively asserted.” It consisted partly of canons and partly of introductory and explanatory dissertations on the matter of the canons and had been duly sanctioned in the Convocation of 1610. It was, however, a strange oversight in Sancroft's party to publish the book, as there are several canons in it which clearly lay down that a de facto government is, when completely established, to be held in the light of a de jure government; and it was upon the very grounds set forth in this book that Dr. Sherlock took the oaths to King William.
Sancroft was a patron of Henry Wharton (1664-1695), the divine and church historian, to whom on his deathbed he entrusted his manuscripts and the remains of Archbishop Laud (published in 1695). From 5 August 1691 till his death two years later, he lived a very retired life in his home village. He was buried in the churchyard of Fressingfield, where there is a Latin epitaph to his memory.