The flotilla was reformed 1 January 1940 allocated to the Mediterranean Fleet until 28 January 1943. It was part of Force C at the Battle of Cape Matapan, 27 to 29 March 1941. The Flotilla was engaged at Battle of the Tarigo Convoy on 16 April 1941. It took part in the Second Battle of Sirte, (22 March 1942). It was next transferred to the Levant Command then at Alexandria until 2 July 1943. Reassigned back to the Mediterranean Fleet 1 October 1943. It was next operating with Force H where it remained until January 1944 then was de-established.