Clinton commanded the English fleet during the invasion of Scotland by Edward Seymour and provided naval artillery support at the Battle of Pinkie on 15 September 1547. In August 1548 he sailed into the Firth of Forth and scattered French and Scottish ships near Leith. He then landed 500 men to burn the ships in the harbour of Burntisland and contemplated fortifying the harbour for English use. He was aboard the "Great Barque".