On 1 January 1939, the Squadron re-mustered as a fighter unit but retained Hawker Hinds until the beginning of the war when it received Fairey Battle's and then Hurricanes. These were soon given up in favour of Spitfires. All civil flying had now ceased, apart from de Havilland Dragon’s on army co-operation work and eighteen of Hooton's considerable population of light aircraft were immobilised and stored under the old grandstand. All were destroyed in July 1940 in a disastrous fire.
During WW2 the station was used by Coastal Command, operating patrol flights over the Irish Sea from South Wales to Cumbria. An important function of Hooton's war effort was the assembly and repair of RAF aircraft, undertaken by Messrs Martin Hearn Ltd founded on the site in the mid-thirties by a former wing-walker with Cobhams Flying Circus.
During the retreat from Dunkirk, many types of aircraft landed at Hooton Park and as soon as they touched down, each aircraft was pulled off the runway to a parking position freeing up the runway for the next aircraft to land. Examples of all type of machine were in evidence, the list including Gloster Gladiators, Walruses, Douglas C-47s (DC3s or 'Dakotas'), Bostons, Blenheims, Swordfish to name just a few.