The station opened in February 1942 as a satellite station to RAF Coningsby. In August 1943 it became No. 54 Base Substation. After victory in Europe the airfield was used as an assembly and kitting out point for Tiger Force (a proposed heavy bomber force for the far east). After the end of the Second World War and with the move of No. 617 Squadron to RAF Waddington the airfield was closed.

97 Squadron transferred to Woodhall Spa on 1 March 1942. As one of the earliest squadrons to be equipped they were heavily involved with the early operations with this aircraft, including the low level mission to bomb the MAN diesel engine factory in Augsburg on 17 April 1942. New Zealander Les Munro , flew on 617 Squadron's Dambuster raid , served with 97 Squadron at Woodhall Spa before being posted to Scampton to join 617 in early 1943. He came back to Woodhall Spa in January 1944 when 617 moved there for the rest of the war. 97 Squadron moved to RAF Bourn in 1943 leaving behind 3 crews.

617 Squadron who arrived with 34 Avro Lancasters and 2 de Havilland Mosquitoes, the latter being used for low level target marking. 617 Squadron remained here until the end of hostilities and pioneered the use of the Tallboy and Grand Slam bombs from the airfield.

627 Squadron The low level target marking that had been developed by 617 Squadron was so successful that 627 Squadron, a Mosquito unit were loaned to 5 Group to operate in this role. The squadron arrived at Woodhall Spa on 14 April 1944 and stayed until the end of the war.