Thomas Thomson (died 1572) was a Scottish apothecary in Edinburgh who served the court of Mary, Queen of Scots.
Thomson was active in the 1540s and supplied medicines to Regent Arran, his daughter Barbara, Lady Gordon, and Cardinal Beaton.
At his death the "drugs, unguents, plasters, spices, and other medicaments" in his shop and cellar were worth £300 Scots.
Robert Henryson complained in 1575 that he was still owed money, and the price of a chest of gray sugar and a barrel of olive oil from Thomson's estate.
In 1552 they bought the lands of East and West Duddingston from her brother Robert Barton.