Commander John Shortland (1739–1803) was a Royal Navy officer known for being the agent for transports of First Fleet and for exploring and charting islands in the South Pacific.

Shortland after leaving the Cape of Good Hope, with Phillip on HMS Supply with three of the fastest transports, Alexander, Friendship and Scarborough, sailed ahead of the rest of the fleet as an advance party arriving at Botany Bay, Australia, on 17 January 1788.

After remaining in Australia until 14 July, he sailed for England in the Alexander, carrying the first dispatches of Governor Phillip to the Secretary of State for Foreign Affairs Francis Osborne, accompanied by the Borrowdale, Prince of Wales and Friendship.

He strongly urged the Admiralty to have the eastern coast of Australia properly charted, and as a result the Secretary of State for Foreign Affairs dispatched Matthew Flinders in HMS Investigator.

Shortland was promoted to commander in 1790 and, after further active service, retired to Lille, France, where he died in 1803.