Naylor was recalled to the navy soon after the start of the Second World War and returned to duty at "Pembroke" on 11 September 1939. He was posted to HMS "Calliope", the Royal Naval Reserve base on the Tyne, on 27 November 1939. He served aboard the armed yacht "Star of India" for two days from 8 April 1941. Naylor commanded the landing ship "Karanja" from 6 September 1941 until 17 August 1942. This included the 5 May landings at the start of the Battle of Madagascar, for which he was mentioned in dispatches on 25 August 1942 "for bravery and enterprise while serving in H.M. Ships, Transports and Royal Fleet Auxiliaries in the successful operations which led to the surrender of the important base of Diego Suarez". Afterwards Naylor commanded HMS "Salsette", a Royal Navy combined operations base at Lake Khadakwasla in India, with the acting rank of captain. He held this position until transferred to command the shore establishment HMS "Braganza" in 1943.