On 17 April 1945, near the end of the Second World War, a No. 57 Squadron Lancaster was being loaded with bombs when a fully armed bomb was unintentionally dropped onto the tarmac. Because the bomb had had its fuse inserted it detonated, setting off the rest of the Lancaster's bombload. A massive explosion killed three airmen, injured 16 others, wrote off six other Lancasters beyond repair and badly damaged a nearby aircraft hangar. The final wartime raid from East Kirkby was flown on 25 April 1945. In total, 212 operations were carried out during the war, from which 121 Lancasters did not return. Another 29 aircraft were lost due to operational crashes or accidents.
Post war use
No. 630 Squadron disbanded in July that year and its place was taken by No. 460 Squadron RAAF from RAF Binbrook. This squadron joined No. 57 for transfer to the Far East as part of Tiger Force. In the 1950s, the airfield was used by the United States Air Force for Air Rescue squadrons for four years. The station closed in 1958. It was sold by the government in 1964.
The control tower is believed to be haunted. The airfield was featured in a 1980s BBC series about World War II airfields. Much of the runway is still intact today but mainly used by local farmers as hard standing and by model aircraft enthusiasts. Occasional civilian light aircraft have landed on the remaining runway and the airfield still appears on Civil Aviation Maps as a diversion emergency landing location. A memorial to the fallen can be found outside the main gate where the guard house once stood. RAF East Kirkby was investigated by the Most Haunted team in 2003 for their third series on Living TV now called Sky Living. Yvette Fielding and her team investigated the museum and site for alleged paranormal activity. The episode was transmitted on Tuesday 7 October 2003 on Living TV. It was the first episode of the third series of the paranormal investigation show Most Haunted. In 2008 the museum opened an unlicensed part-grass and part-concrete landing strip for visiting military and civil aircraft. No aircraft should land without contacting the museum's owners first. Air traffic control on flying display days is from RAF Coningsby and there is a six-mile "no fly" exclusion zone around East Kirkby on display days.