On 14 September 1939, eleven days after the outbreak of the Second World War, McNicoll was posted to HMS "Victory", the flagship of Admiral Sir William James, the Commander-in-Chief, Portsmouth. In April 1940, McNicoll was transferred to the light cruiser as a member of the ship's commissioning crew. During McNicoll's time aboard the ship, it was severely damaged by a torpedo in operations on 1 September and barely made it back to harbour. McNicoll ultimately served on "Fiji" for six months before being attached to , a submarine depot ship stationed at Alexandria, Egypt, in October 1940. In this post he was made torpedo officer of the 1st Submarine Flotilla operating in the Mediterranean theatre. In addition to his standard duties, McNicoll was regularly involved in rendering safe captured enemy ordnance. On one such occasion, he was tasked with disarming the captured Italian submarine "Galileo Galilei", which entailed removing the inertia pistols from eight torpedoes that had badly corroded. As a consequence of his "gallant and undaunted devotion to duty" in this action, McNicoll was awarded the George Medal and presented a Commander-in-Chief's Commendation. His decoration was promulgated in a supplement to the "London Gazette" on 8 July 1941.