Neale moved to the National Football League (NFL), serving as head coach of the Philadelphia Eagles from 1941 to 1950. From 1944 through 1949, Neale's Eagles finished second three times and in first place three times. The Eagles won the NFL Championship in 1948 and again in 1949, and became the first team to win back-to-back titles since the 1940-41 Chicago Bears by shutting out their opponents, beating the Chicago Cardinals 7–0 in the snow-ridden 1948 NFL Championship Game and the Los Angeles Rams 14–0 in the 1949 NFL Championship Game in a driving rain storm. It was the last championship for the Eagles until 1960. His offense was led by the passing of quarterback Tommy Thompson, the pass catching of future Hall of Fame end Pete Pihos, and the running of another Hall of Famer, Steve Van Buren. He tallied a mark of 66–44–5 including playoff games in his ten seasons with the club. Neale was inducted into the College Football Hall of Fame in 1967 and the Pro Football Hall of Fame in 1969. Both inductions recognized his coaching career.