Jefferson was a P-51 Mustang pilot assigned to the all-Black 332nd Fighter Group. He completed 18 long range escort missions in 1944, until he was shot down by ground fire on 12 August 1944. Jefferson was taken prisoner of war and imprisoned for eight months at Stalag Luft III. Despite his skin colour he recalled being treated the same as the white officers by his captors. 

Towards the end of the war Jefferson was moved to Stalag VII-A, and marched to Munich, where he was liberated by the US Third Army. He returned to the US aboard the RMS Queen Mary in 1945, later commenting that his racially charged treatment upon his homecoming was inferior to his treatment by the Nazis. 

Jefferson served at Tuskegee field, Alabama as an instrument instructor, until its closure in 1946, then served in the US Air Force reserves. He retired as a Lieutenant Colonel in 1969.