At the start of the Second World War No 3 Squadron was posted as part of Fighter Command to RAF Station Biggin Hill equipped with the Hawker Hurricane. It briefly deployed to France in support of the British Expeditionary Force following the German attack on the West in 1940, being forced to withdraw after 10 days, having claimed 60 German aircraft for the loss of 21 of its own.
Between 06/41 to 08/41 No 3 Sqn moved from Martlesham Heath to RAF Stapleford Tawney operating 4 canon Hurricane 11s in 'Rhubarb' attacks on defended ground targets and shipping in northern France & Belgium. (Source Sqn logs National Record Office>.
On 21 July 1940 "B" flight was detached to form the nucleus of the newly formed No. 232 Squadron. Once back up to strength, No. 3 Squadron was used as air defence for the Royal Naval base at Scapa Flow, remaining in Scotland until April 1941, based at RAF Station Wick in Northern Scotland. The squadron then co-operated with "Turbinlite" searchlight equipped Douglas Havocs in the night fighter role.
In February 1943 it re-equipped with the Hawker Typhoon for fighter-bomber and anti-shipping strikes. It re-equipped in March 1944 with the new Hawker Tempest fighter, operating over the Normandy beach-head and against German V1 flying bombs, claiming 288 V-1s shot down.
It then deployed across the Channel, flying as part of the 2 TAF fighting through the low countries and into Germany. Amongst its pilots was F/L Pierre Clostermann, who flew with 3 Squadron from March 1945 until the end of the war in Europe.