Neptune was one of the notorious Second Fleet ships to Port Jackson. Built in the River Thames in 1779, at 809 tons she was the largest ship of the fleet. In company with Surprize and Scarborough she sailed from England with 421 male and 78 female convicts on 19 January 1790. Her master was Donald Traill and surgeon was William Gray. She arrived at the Cape of Good Hope on 13 April 1790, and spent sixteen days there, taking on provisions, and twelve male convicts from HMS Guardian which had been wrecked after striking an iceberg. She and Scarborough were parted from Surprize in heavy weather and arrived at Port Jackson on 28 June 160 days out from England. During the voyage 158 convicts died (31%) and 269 (53%) were sick when landed.
The treatment of convicts aboard the Neptune was unquestionably the most horrific in the history of transportation to Australia. Convicts suspected of petty theft were flogged to death; most were kept chained below decks for the duration of the voyage; scurvy and other diseases were endemic; and the food rations were pitiful.
Upon their return to England, the Master, Donald Traill, and Chief Mate, William Ellerington, were privately prosecuted for the murder of an unnamed convict, along with a seaman named Andrew Anderson and a cook named John Joseph. After a trial lasting three hours before Sir James Marriott in the Admiralty Court, the jury acquitted both men on all charges "without troubling the Judge to sum up the evidence". There were no public prosecutions.
Amongst the arrivals on this voyage was D'Arcy Wentworth. John Macarthur, his wife Elizabeth, and their son Edward Macarthur left England on Neptune but transferred to Scarborough after a quarrel with the captain. A photograph of Edward Macarthur exists, and is the only known photo of a passenger on Neptune.