Alexander Thomson (c. 1593 – 1646) was a minister in the Church of Scotland in the early 17th century during the lead up to the Wars of the Three Kingdoms.
He was the son of Rev Alexander Thomson, minister of Stonehouse in Lanarkshire.
In 1638 the General Assembly of the Church of Scotland declared the National Covenant and defied King Charles I's Episcopalian policies.
Mr Thomson declined to follow this demand, and sided with the King, not only using the new prayer book in his services, but defending its use more widely.
He had another son, William, and a daughter Margaret, who married James Hamilton, the Bishop of Galloway, further confirming his Episcopalian sympathies.