Mather was assistant secretary of both Manchester City and Bolton Wanderers before taking the manager's job at Bolton at the beginning of the First World War, remaining at the club until 1915 when he was called up by the Royal Navy. He remained as manager, in name only, until July 1919, his duties being taken on, and then over, by his assistant Charles Foweraker. After his national service he moved to Southend United as secretary-manager. He spent three years at the "Shrimpers" before joining Stoke City in October 1923. Stoke had just been relegated from the First Division and had to get over the shock of seeing Jock Rutherford quit the club after just four weeks in charge. Mather's first season in charge saw Stoke finish in 6th position and he decided to move on a number of players at the end of the season. This didn't go down well with some of the released players who to smash up the offices at the Victoria Ground and caused a considerable amount of damage.
Things didn't improve quickly and Stoke suffered relegation to the Third Division North in 1925–26 season. But he spent his transfer budget well and Stoke gained an instant return to the second tier. The goals of Charlie Wilson proved invaluable as Stoke began to start pushing for a return to the First Division. Mather gave Stanley Matthews his debut in February 1932. After a number a failed attempts Stoke finished as Second Division champions in 1932–33. Mather remained in charge of Stoke for two more seasons before Bob McGrory took over and Mather left in 1935 to join Newcastle United. Anecdotal evidence suggests that Mather attempted to encourage Matthews to join him at Newcastle, but Matthews declined.