James Paton (1522 – 1596) was a 16th-century Scottish cleric from Ballilisk, an estate in the parish of Muckhart, west of Kinross.
At the Scottish Reformation of 1560 he adopted the Protestant stance, and certainly by January 1565 is listed as minister of Muckhart parish, which was then in Perthshire.
This later brought him into disrepute with the General Assembly, as did his failure to proceed against the allegedly Catholic John Stewart, 4th Earl of Atholl.
In December 1580 he was accused of conspiracy and treason and Paton failed to defend himself satisfactorily, and thereafter a decree was made depriving him of his bishopric.
His descendants stayed in Muckhart until 1760 when James and Andrew Paton left to live in Alloa, working as weavers and dyers.