He was first sent to Magdalen Hall, Oxford, whence he was removed, to save expense, to Trinity College, Dublin There he graduated Oxford Master of Arts (MA Oxon) in 1633. Having entered holy orders, he became minister of several small united parishes in Ireland, where he remained till the breaking out of the rebellion of 1641. Upon James Butler, 1st Marquis of Ormonde's truce with the rebels (15 September 1643), Sherlock returned to England as chaplain of one of the regiments sent by the marquis to aid King Charles in his struggle with parliament. He was present at the Battle of Nantwich on 25 January 1644, in which Thomas Fairfax completely defeated John Byron, 1st Baron Byron and captured many prisoners. Among these was Sherlock, who, on regaining his liberty, made his way to Oxford, where he became chaplain to the governor of the garrison, and also a chaplain of New College. In consideration of several sermons that he preached, either at court or before the Oxford parliament, the degree of Bachelor of Divinity (BD) was conferred upon him in 1646.