Boyle returned to Ireland on the outbreak of the rebellion in 1641 and fought with his brothers against the Irish rebels at the battle of Liscarroll in September 1642. Boyle and the English in Ireland were left vulnerable by the outbreak of the English Civil War. Although initially under the command of the Royalist Marquis of Ormonde (later James Butler, 1st Duke of Ormonde), Lord Broghill consented to serve under the parliamentary commissioners in Cork against the Irish Confederates. Boyle fought with the Parliamentarians until the execution of the king, when he retired altogether from public affairs and took up his residence at Marston in Somerset.