In 1659, Chaplin was commissioner for militia for Suffolk and was elected Member of Parliament for Bury St Edmunds in the Third Protectorate Parliament. He was commissioner for assessment for Suffolk in January 1660 and commissioner for militia for Bury in March 1660. In April 1660 he was re-elected MP for Bury St Edmunds for the Convention Parliament when he was involved in a double return. He was allowed to take his seat and then unseated.
