Gordon first studied at St Leonard's College, St. Andrews. In June 1565 he was sent to pursue his education in France, having a yearly pension granted him by Mary, Queen of Scots, payable out of her French dowry. He spent two years at the universities of Paris and Orleans. On 4 January 1568 he was confirmed by royal charter in the bishopric of Galloway and abbacy of Tongland, vacated in his favour by his father; the charter specifies his skill in classical and oriental tongues. At this time he was in France, in the service of the Protestant leader, Prince Louis of Conde, but he soon came to England, entered the service of Thomas, Duke of Norfolk, and attended him at the conferences of York (October 1568) and Westminster (November 1568), held for the purpose of considering Mary's guilt.