In October 1643, Selden was appointed by Commons to take control of the office of Clerk and Keeper of the Records in the Tower, which duty passed to the Master of the Rolls in 1651. In 1645 he was named one of the parliamentary commissioners of the admiralty and was elected master of Trinity Hall, Cambridge, an office that he declined to accept. In 1646, he subscribed to the Solemn League and Covenant and, in 1647, was voted £5000 by the parliament as compensation for his pains under the monarchy.