"Scarborough" went back to New South Wales with the notorious Second Fleet. With "Surprize" and "Neptune" she sailed from England with 253 male convicts on 19 January 1790. Her captain was again John Marshall and the surgeon was Augustus Jacob Beyer. She arrived at the Cape of Good Hope on 13 April 1790, and spent 16 days there, loading food and other items. She also picked up eight male convicts from HMS "Guardian" which had been wrecked after hitting an iceberg. She and "Neptune" were parted from "Surprize" in heavy weather and arrived at Port Jackson on 28 June, 160 days out from England. During the voyage, 73 convicts died (28%) and 96 (37%) were very sick when landed.