In January 1649, Penington was appointed a commissioner of the High Court of Justice at the trial of King Charles, but he was not one of the signatories of the King's death warrant. He served on the Rump's Council of State and on several government committees. He was made a knight in 1649. From 1650 he was the sole representative of the City of London in the Rump Parliament until it was forcibly ejected by Oliver Cromwell on 30 April 1653.