World War II, with its increasing need for trained pilots, helped to reestablish Ellington Field as an active facility. Rep. Albert Thomas, one of Houston's representatives in the United States House of Representatives, pushed for rebuilding Ellington as a pilot training center. Beyond the area's excellent weather for flying, Thomas argued that the Houston area's petroleum refineries, upon which the war effort depended, would need military protection in the region. In 1940, construction began on a much-expanded Ellington Field, which eventually included five control towers, two 46,000-square-foot (4,300 m2) hangars, the most modern medical complex in south Texas and 74 barracks.
Ellington Field was the site for advanced flight training for bomber pilots. Initial plans called for the training of 2,800 bomber pilots per year at Ellington Field or about ten percent of the total number of pilots trained throughout the United States. Beginning at five-week intervals, classes of 274 cadets entered the 10-week course. Cadets moved from the AT-6 to the more complex twin-engine AT-10 or AT-11. At that level, cadets were taught how to fly the larger multi-engine aircraft. After successful completion of the advanced training course, graduates were transferred to different airfields for more training in actual bombers. Eventually the USAAC Advanced Flying School was transferred to Blackland Army Airfield in Waco.
Ellington Field was also a site for the USAAC, later USAAF, Bombardier School, also known as "the Bombardment Academy of the Air." At Ellington Field, officials planned to train 4,480 bombardier cadets per year. Bombardier cadets spent most of their time during the 10-week course in the classroom learning the skills necessary to accurately drop bombs on enemy targets. Hands-on training for the bombardier cadets took place over the Gulf of Mexico. In AT-10s or AT-11s, bombardier students practiced bombing several small islands in Matagorda Bay or small target boats anchored in the bay. The Bombardier School remained at Ellington Field until 1942.
In 1943, Ellington Field became the site for advanced navigator training when the Army Air Forces Training Command transferred the Navigator School from Mather Field, California to Houston. The USAAF Navigator School consisted of a rigorous 18-week course consisting of instruction in celestial navigation and dead reckoning. To complete the course, cadets were required to have 100 hours in navigating both local and long-range flights. By 1944, the Navigator School used instructors with combat experience to teach classes. Veteran navigators from every theater of operations lectured cadets at Ellington Field. These lectures were invaluable to cadets because the veteran navigators gave their students insights into navigating under combat conditions and life overseas. From 1941 to 1945 the Navigator School graduated 4,000 USAAF navigators that were assigned to every theater of operations during the Second World War.
By the end of 1943, more than 65 women who served in the Women's Army Corps were also stationed at Ellington. The WACs worked in noncombat Army jobs in order to free men for combat duty. "By taking over an Army job behind the lines, she frees a fighting man to join his fellow soldiers on the road to Victory," stated WAC director Colonel Oveta Culp Hobby. With the end of World War II, Ellington served primarily as a reserve air base from the end of the war in 1945 until 1948.