John Duncanson (ca. 1530–1601) was a Scottish clergyman. He was tutor and chaplain to King James VI, and Moderator of the General Assembly of the Church of Scotland in 1574 and 1576.
Duncanson married Janet Watson. Their eldest son was James Duncanson (ca. 1564–1624), Minister at Alloa, Clackmannanshire, who married Helen Livingston.