Major-General Sir Thomas Morgan, 1st Baronet (1604 – 13 April 1679) was a professional soldier from Wales who fought for Parliament during the Wars of the Three Kingdoms.

As deputy Commander-in-Chief, Scotland, he played an important role in the 1660 Stuart Restoration and was rewarded with being made a baronet.

At 16, having at that time little knowledge of any language but Welsh, Morgan enlisted in Sir Horace Vere's Protestant volunteer expedition which fought in the Thirty Years' War.

Morgan fought in the Low Countries and in particular assisted the Dutch in the decisive victory at the battle of the Slaak in 1631.

He rejoined Monck in Scotland, and played a conspicuous part in the Stuart Restoration in Edinburgh.