 During the early years of World War II, Watson-Jones remained a civilian consultant to the Royal Air Force.He set up ten units of 100–150 beds each across the United Kingdom to house recovering pilots; his emphasis on rehabilitation meant that many were able to return to active service.In 1942, he established the Department of Orthopaedics and Accidents at the London Hospital and in 1945 he was knighted for his service to the war efforts.