After the outbreak of the Second World War, he was given command of HMS "H31" which he commanded from February until August 1940. Wanklyn sailed on patrol in the North Sea, during which he sank one vessel. In August 1940 he was given command of newly commissioned HMS "Upholder". In December 1940 the submarine was reassigned to the Mediterranean. Wanklyn began the first of his patrols in January 1941 and remained on operations in the Battle of the Mediterranean for the remainder of his career.