In May 1883, Welldon was appointed master of Dulwich College. In the short time he held this position he did much for the college, including the creation and institution of its school song "Pueri Alleynienses" which is still in use today. He resigned in July 1885 to take up the position of headmaster of Harrow School, which he held from 1885 to 1898. He was disliked by many of the masters as an autocratic administrator, but was more popular with the boys, by whom he was known as "the Porker."