After his college playing days were over, Noble went on to coach basketball, football, and most notably baseball at the college level for three different schools in his home state; Mississippi College, The University of Mississippi, and his alma mater Mississippi A&M.
His first coaching job was as the head football coach at Mississippi College in 1916. While there he earned his first coaching victory when he led the Choctaws to a 13–6 upset over Mississippi State in a game played in Aberdeen, Mississippi. The Choctaws finished the season with a record of 4-3
In 1917 Noble became the head football coach at the University of Mississippi (Ole Miss), a position he held for two seasons. During his two years as the Rebels' head coach he compiled a record of 2–7–1 and went 0–3 against his alma mater, Mississippi A&M. He holds the distinction of having been the only head coach to lose two Egg Bowls in one season (1918). For the 1918–19 season he served as the head basketball coach at Ole Miss going 0–3. He had his most success in Oxford as the baseball coach compiling an overall record of 10–4 in the 1918 and 1919 seasons.
Starting in 1920 Noble took over as skipper of the Mississippi State baseball team, a position that he held for 26 seasons until 1947 (MSU had no baseball team in 1944 and 1945). As head baseball coach he compiled a record 267–201–9 and won three Southern Intercollegiate Athletic Association championships. During his time as head baseball coach he awarded Dave "Boo" Ferris the first full baseball scholarship in Mississippi history. Noble also served one season as the Bulldogs' head football coach going 3–4–2 in 1922, including a victory over his former squad from Ole Miss.
From 1938 to 1959, Noble was also the athletic director at Mississippi State. During his tenure as athletic director he made several notable hires. Among those were football coaches Murray Warmath, Darrell Royal, and Allyn McKeen. McKeen left as MSU's all time winningest head coach and is the only MSU coach elected to the College Football Hall of Fame. He hired basketball coach Babe McCarthy who won three SEC championships and defied state authorities to take MSU to its first NCAA Basketball Tournament in 1963. In 1953 he hired Jack Cristil who would go on to be the "Voice of the Bulldogs" for 58 years.
Speaking on his time spent in Oxford Dudy Noble once told a Tennessee sports writer: “I already know what hell is like. I once coached at Ole Miss.” Noble once owned a bird dog, a lazy mutt that refused to hunt. Dudy Noble named him “Mr. Ole Miss.”
National champion Postseason invitational champion Conference regular season champion Conference regular season and conference tournament champion Division regular season champion Division regular season and conference tournament champion Conference tournament champion