When Richard Molyneux resigned in 1901 William Cuff was asked to replace him in taking charge of club affairs, which he agreed to readily, even though it meant he would have to give up his place on the board, which he had occupied since 1895. Cuff's association with the club went back to the St. Domingo's days; when, as a ten year old, he would cheer on the club he would serve with distinction for many years.

Cuff was responsible for keeping the club going during the First World War, with football being postponed most clubs played in regional leagues. It turned out to be an exceptionally busy, anxious and exacting time for William Cuff.

He had been educated at Liverpool College and was admitted to the legal profession in 1893; the demands of his work as a solicitor had forced him to resign as club secretary in 1918. However just three years later he was back at the club, this time as chairman, a position he would hold until he was selected as the chairman of the Football Association in 1938.

His lasting legacy for football in general was the formation of an organized league for the reserve sides of each club and the central league was born in 1911.

William Cuff's record during his time in charge of Everton team affairs was impressive, 1 League title & 4 runners up, 1 FA Cup win, 1 runners up & 2 losing semi finals. In 1925 Cuff was instrumental in what was arguably Everton's greatest signing when he instructed secretary Tom McIntosh to secure the services of an 18 year old from Tranmere Rovers called William Ralph Dean.