This continued until August 1940 when they were reassigned to the Mediterranean, where part of their duties were the ferrying of supplies between Alexandria and the besieged island of Malta.

Attached to the 1st Submarine Flotilla based in Alexandria, and under the command of Lieutenant-Commander Edward Christian Frederick Nicolay DSO RN (see Nicolay (family)), she sank the 3,867-ton Italian tanker Maya 5 nautical miles (9 km) south of Tenedos on 5 September 1941, and on 2 October, the 2,086-ton merchant ship Castellon west of Benghazi.

Perseus sailed from Malta for Alexandria on 26 November 1941 with instructions to patrol waters to the east of Greece during her passage.

Of the 61 on board, the only survivor was 31-year-old leading stoker John Capes, one of two non-crew members who were hitching a lift to Alexandria.

The wreck, at 52 metres (171 ft) below the surface, was discovered and surveyed in 1997 by a dive team led by Kostas Thoctarides.