In 1699 Clarke published two treatises: "Three Practical Essays on Baptism, Confirmation and Repentance" and "Some Reflections on that part of a book called Amyntor, or a Defence of Milton's Life, which relates to the Writings of the Primitive Fathers, and the Canon of the New Testament". In 1701 he published "A Paraphrase upon the Gospel of St Matthew", which was followed, in 1702, by the "Paraphrases upon the Gospels of St Mark and St Luke", and soon afterwards by a third volume upon St John. They were subsequently printed together in two volumes and passed through several editions.