The squadron was initially equipped with Fairey Albacores on its formation at RNAS Lee-on-Solent, and then moved to Scotland to operate anti-submarine patrols with RAF Coastal Command. They embarked aboard in July 1941 and carried out an attack on Kirkenes, Norway. Five of the squadron's aircraft were lost in the attack. The squadron was then regrouped and sailed to Gibraltar in August aboard. They were then transported to Hal Far, Malta aboard HMS Ark Royal. From there the squadron attacked enemy shipping attempting to transport supplies to the Axis forces in Libya. In March 1942 they and 830 Naval Air Squadron formed the Naval Air Squadron Malta, which went on to attack enemy warships and convoys operating in the Mediterranean. Re-supply problems, partially alleviated by the Malta Convoys led to the number of operational aircraft being reduced to just two. In December 1942 the remnants of 826 and 830 squadrons were absorbed. 828 and 821 Naval Air Squadrons attacked shipping in May 1943, and provided flare illumination for naval bombardments of Pantellaria. In July, from Hal Far on Malta, 828 squadron's Albacores supported the Allied invasion of Sicily. 828 then moved to Monastir in Tunisia, where they disbanded in September 1943. Together 828 and 830 squadrons had sunk 30 enemy ships and damaged another 50.
828 Squadron was re-formed as a torpedo bomber reconnaissance squadron in March 1944. Equipped with 12 Barracuda IIs they joined the 2nd Naval Torpedo Bomber Reconnaissance Wing and joined the Home Fleet aboard in August that year. They briefly transferred to in August 1944 and carried out attacks on the German battleship Tirpitz as part of Operation Goodwood. They were briefly at RNAS Hatston, before re-boarding HMS Implacable and carrying out attacks on enemy shipping off the Norwegian coast in October. 828 Squadron was re-equipped with 21 Grumman Avenger Is and IIs in January 1945, and then joined HMS Trumpeter. They were back aboard HMS Implacable by March 1945, and sailed with her to Ceylon, subsequently disembarking at Trincomalee in April 1945. 828 Squadron then joined the 8th Carrier Air Group and carried out attacks on Truk and the Japanese mainland. After the Japanese surrender the squadron returned to Nowra on 25 August 1945, and remained there until May 1946.
