Thompson is more famous for his executive role in the Dodger organization. He became a minor league manager after his playing days, and was selected as assistant farm director of the Brooklyn Dodgers in 1946. In 1950, he was named vice president, and was put in charge of all minor league operations. He stayed with the team through its move to Los Angeles, and in 1968, he was named executive vice president and general manager. Thus Thompson witnessed the zenith of Dodger baseball, from the "Boys of Summer" period of the 1940s and 50s, to the "Pitching, Speed, Defense" teams of Koufax, Drysdale, and Wills in the 1960s.