Upon his return Clerke published an account of encountering Patagonian giants, a hoax which the Dictionary of Canadian Biography attributed to his high spirits.

He continued the expedition's exploration of the Northern Pacific coast, searching for a navigable Northwest Passage.

On 10 August 1779, Clerke wrote in a letter to Sir Joseph Banks that, "The disorder I was attacked with in the King's bench prison has proved consumptive, with which I have battled with various [unclear] although without one single days health since I took leave of you ... it has now so far got the better of me that I am not able to turn myself in bed, so that my stay in this world must be of very short duration.

The expedition then sailed via China and the Sunda Strait to Cape Town, returning to England in August 1780.

[6] In 1913, the British Admiralty erected a small obelisk in Clerke's honour at Petropavlovsk-Kamchatsky, Russia, with an inscription in English.