He was not elected to the Short Parliament of 1640; but to the Long Parliament, summoned in the autumn, he was returned without opposition for Oxford University. He opposed the resolution against episcopacy which led to the exclusion of the bishops from the House of Lords, and printed an answer to the arguments used by Sir Harbottle Grimston on that occasion. He joined in the protestation of the Commons for the maintenance of the Protestant religion according to the doctrines of the Church of England, the authority of the Crown, and the liberty of the subject. He was equally opposed to the court on the question of the commissions of lieutenancy of array and to the parliament on the question of the militia ordinance. In the end, he supported Parliament against King Charles, because, according to him, Charles was certainly acting illegally; but Selden was not certain if Parliament was doing the same.