On the outbreak of the Second Desmond Rebellion in 1579, Stanley was promoted to captain under Sir William Drury, lord justice of Ireland, who knighted him at Waterford for his service in penetrating Limerick in pursuit of the followers of Gerald FitzGerald, 14th Earl of Desmond. He fought in the battle of Monasternenagh and defended the town of Adare. In 1580, he enlisted troops in England and led them to the rebellious province of Munster; but the new lord deputy, Lord Grey, quickly recalled him to the Pale to help put down the rebellion that had broken out in the vicinity of Dublin.