After being promoted lieutenant of the prize ship Manila by Vice-Admiral Sir Samuel Cornish following the capture of Manila on 16 December 1762, Waghorn served in the Liverpool 32, Captain Edward Clark, returning to England in August 1763. He spent the next fourteen years on half-pay, during which time he was employed in the merchant service.
In the spring of 1778 he was appointed to the Prince George 98, Captain Sir John Lindsay, after that officer had relinquished the command of the Victory 100 to Admiral Hon Augustus Keppel, but two years later he became the eighth lieutenant of the Victory. During the time he served with her she was employed successively as the flagship of Admiral Sir Charles Hardy, Admiral Francis Geary and Vice-Admiral Sir Hyde Parker in the Channel fleet. By natural progression he became her first lieutenant in 1781, and following the Battle of the Doggersbank on 5 August, where despite being wounded he remained on deck, he was placed in temporary command of the Artois 40. He was then quickly promoted commander of the sloop Fly 16 on 15 August. .
On 6 April 1782 Waghorn was posted captain of the Royal George 100 with the flag of Rear-Admiral Richard Kempenfelt, and he served in the Channel fleet campaign from April-August. He was thereafter with Vice-Admiral Hon. Samuel Barrington s squadron that blockaded the Texel, but tragically the Royal George sank at her moorings at Spithead on 29 August with the loss of approximately a thousand men, including his own son and scores of dockyard artificers. After desperately trying to rescue the admiral Waghorn himself had to rely on the intervention of a seaman to prevent him from drowning, and during the incident he suffered many contusions. At the subsequent court martial into the loss of the Royal George he and his officers were acquitted for the loss of their ship.
He thereafter remained on half-pay until September 1783 when he was appointed flag captain to his old friend, Commodore Sir John Lindsay, aboard the Trusty 50 in the Mediterranean. In July 1785 the Trusty was paid off.
Captain Waghorn died on 17 December 1787 whilst on half-pay, and having long suffered from gout.
He was married and had issue, his son Martin, a midshipman, being a victim of the Royal George tragedy. His fourth daughter, Eliza, became Admiral Hon. Sir Henry Blackwood s second wife. At the time of his death his address was given as St. Mary Newington, Surrey.
Waghorn was respected for his abilities as a seaman and an officer. A financially poor man, he was constantly in need of employment.