On 14 Sept. 1640 he was at York, and wrote a long letter to Sir John Lambe, describing the movements of the royal army.
By his wife Anne, who died in 1655, he had four surviving children- John, Oliver, Elizabeth and Margaret.
Wherein the Vicar of Gr[antham], being dead, yet speaketh, and pleadeth out of Antiquity against him that hath broken downe his Altar,' London, 1637.
Among the king's pamphlets in the British Museum is 'The Petition and Articles exhibited in Parliament against John Pocklington, D.D., Parson of Yelden, Bedfordshire, Anno 1641,' London, 1641; reprinted in Howell's 'State Trials'.
On 12 February 1641 he was sentenced by the House of Lords never to come within the verge of the court, to be deprived of all his preferments, and to have his two books, 'Altare Christianum' and 'Sunday no Sabbath,' publicly burnt in the city of London and in each of the universities by the hand of the common executioner.
When Pocklington was deprived of his preferments, William Bray, who had licensed his works, was enjoined to preach a recantation sermon in St. Margaret's Church, Westminster.