But the end of his term was marred by a row with fans, as he publically fell out with the Wednesdayite supporter group and launched legal action against comments made on an internet messageboard.
In July he launched a scathing attack on some sections of the Hillsborough crowd, calling them "scum" and "cretins" after he claimed to have been verbally abused at a match.
Allen escaped action from the Football Association despite being called to a disciplinary hearing to explain his actions.
An Owls statement said: "The board would like to place on record their appreciation of Mr Allen's significant contribution during his chairmanship."