Jean married secondly at Huntly Castle, on 13 December 1573, Alexander Gordon, 12th Earl of Sutherland, thus becoming the Countess of Sutherland. Alexander was previously married to Barbara Sinclair, daughter of his guardian, George Sinclair, 4th Earl of Caithness; but this relationship had been sour, and ended in divorce when the young Earl of Sutherland came of age, apparently without children. Jean and Alexander together had seven (or possibly eight) children.
Within two years of Jean's second marriage, due to the earl's increasing ill health, Jean ran the vast Sutherland estates from their base at Dunrobin Castle. The earl died on 6 December 1594.