Anderson taught civilian pilot training courses at Howard University, Washington, D.C. In 1940, he joined the faculty at Tuskegee Institute as head of the Civilian Pilot Training (CPT) program. Chief Anderson gave Eleanor Roosevelt a plane ride when she visited Tuskegee in 1941. She was determined to counter the view that African Americans couldn't fly. Their photograph was seen all over the U.S. Mrs. Roosevelt's plane ride gave an enormous boost to black aviation.

The successful CPT under Anderson's leadership was a major factor in the Army Air Corps decision to establish a primary training program at Tuskegee. As chief flight instructor at Tuskegee, he supervised primary flight training for 1,000 African-American pilots at Moton Field.