Following the outbreak of the Second World War, Parkinson's rank was made substantive and was later seconded to the Second New Zealand Expeditionary Force (2NZEF). He was given command of the 4th Field Artillery Regiment and embarked with the First Echelon of the 2NZEF in early 1940. After serving in the initial stages of the Western Desert campaign, for which he was mentioned in despatches, he led the regiment well during the Battle of Greece. He was later awarded the Distinguished Service Order (DSO), gazetted on 14 April 1942, due in part to his service during the battle.
