While at Cambridge he met and befriended Henry Cromwell. His father died the following year, and John Perceval decided that, with wars raging in both England and Ireland, he would remain at university and so remain out of public life to avoid choosing sides in the wars. In 1649, after the execution of Charles I, the rebellion in Ireland was crushed by the New Model Army under the command of Oliver Cromwell. Given Perceval's large holdings in Ireland, he thought it politic to return to protect his interests. This was difficult because his father had opposed the English Independents who were now in the ascendancy.