With US participation in World War II eminent, the military began to train pilots in Wichita Falls again. This time at the new Sheppard Air Force Base, which sprang to life in 1941. It was established to train troops and pilots for the war but was deactivated in 1946 at the war's end.

During the Korean War, the United States Air Force decided to reactive the base and enlarge it to provide a number of new aviation schools. Eventually, a new runway was constructed and later used by B-52 bombers. For a short time, helicopter training was conducted at Sheppard, but as jet pilot training expanded, helicopter training was soon phased out.

After the establishment of the Federal Republic of Germany, the Luftwaffe was rebuilt in 1965. Many new student pilots were sent to the United States for pilot training; first to Luke AFB and then to Williams AFB in Arizona. In August of 1966, Air Training Command and the German government decided to move the German program from William to Sheppard AFB, creating a joint German and American flying training program.

From 1966 to 1981, the German Air Force and Navy trained all of their fighter pilots at Sheppard. Some classes were composed of both American and German students while others were exclusively German. All were taught by both American and German instructors. The Germans sent approximately 100 students per year. In 1979, the Royal Netherlands Air Force joined the program with 20 students per year. 

In 1976, NATO began to consider a joint pilot training program for all NATO countries. For two years the NATO countries debated as to who should be the host. Turkey, Italy, Spain, and the United States were all under consideration. After much negotiation, NATO decided the United States Air Force should host the program - primarily due to its facilities, numbers of aircraft, and established training program. Between 1978 and 1980, battle raged within the United States Air Force as to which base should host the new NATO program. Originally, the final selection was between Columbus AFB, Mississippi, Williams AFB, Arizona, or Laughlin AFB, Texas. Sheppard AFB was not even considered.

Civic leaders in the Wichita Falls area became greatly alarmed at the possibility of losing not only the new NATO program, but also the highly successful German program. Senator John Tower, a Wichita Falls native, took action and soon Congress awarded the new NATO program to Sheppard AFB.

In early 1981, the first meeting of the ENJJPT Steering Committee convened at Randolph AFB for the opening of the program. The first class entered training on October 1, 1981.