Having conscientious objections to taking religious orders, he relinquished his fellowship in 1666, but in 1688 was elected Camden professor of history at Oxford.

As the movement behind the refusal to swear allegiance declined, with the death of William Lloyd who had been deprived of his bishopric, and the decision by Thomas Ken to relinquish his claim to the See of Bath and Wells, Dodwell returned to the Church of England in 1710.

[1] Living on the produce of a small estate in Ireland, he devoted himself to the study of chronology and ecclesiastical polity, providing a defence of the deprived nonjuring bishops.

In his ecclesiastical writings he was regarded as one of the greatest champions of the non-jurors; but the doctrine which he afterwards promulgated, that the soul is naturally mortal, and that immortality could be enjoyed only by those who had received baptism from the hands of one set of regularly ordained clergy, and was therefore a privilege from which dissenters were hopelessly excluded, did not strengthen his reputation.

[4][5]His chief works on classical chronology are: His eldest son, also named Henry Dodwell, was the author of a pamphlet entitled Christianity not founded on Argument, to which a reply was published by his brother William Dodwell (1709–1785), who was concurrently engaged in a controversy with Conyers Middleton on the subject of miracles.