Shortland joined the Royal Navy in 1781 as a midshipman. After served in Quebec and the West Indies. His father, Captain John Shortland (1739-1803), was the person in the Navy who organized many of the details for the First Fleet which took the first convicts to Australia in 1788. He arranged for two of his sons, John and Thomas George Shortland (1771 – 1827), to sail with him on the First Fleet. Shortland was the master's mate on "HMS Sirius" with Captain John Hunter. He was also on the ship when it was wrecked on Norfolk Island in 1790. He left Australia in 1792. 