He took charge as secretary with the side in the Second Division and after finishing third for two seasons, United won promotion in 1905/06. Mangnall's team, skippered by Charlie Roberts and including the legendary Billy Meredith, won the League championship and the FA Cup for the first time, and were the first winners of the FA Charity Shield at the beginning of the 1908/09 season.

Mangnall resigned from United in 1912, moving across town to join Manchester City, where he was responsible for the building of the stadium at Maine Road.

Ernest Mangnall retired from football in 1924 to become a part-time sports correspondent with a Sunday newspaper.