The Tigers confirmed that Duffen has quit the club, just hours after insisting that Phil Brown had not been axed.
A statement on the club’s official website read: “The club has received a letter of resignation from Paul Duffen, executive chairman of Hull City AFC and Superstadium Management Company Ltd, which has been accepted and is effective immediately.
“Paul’s departure is on a totally amicable basis and he leaves with our best wishes as a friend of the club and its directors.
“The club wishes to express its gratitude to Paul for his outstanding contribution as chairman during a period of unprecedented success for Hull City AFC.
“The recruitment process has commenced in respect of the appointment of a new executive chairman and a further statement in relation to this will be issued by the club on Monday, 2nd November.”
Duffen issued his own statement, which read: “When I succeeded Adam Pearson as chairman of Hull City Football Club in June 2007 I was very aware of the responsibility to build on his legacy.
“I articulated an intention to take the Tigers to the previously uncharted waters of the Premier League and to the eternal credit of the players and coaching staff, that seemingly ridiculous ambition was achieved 11 months later thanks to a victorious debut appearance at Wembley in the play-off final.
“The start to our maiden top-flight campaign broke all previous records for a newly promoted side and ensured that 2008 will forever be remembered as the most remarkable year in Hull City’s history.
“Football is a results business and in the same way that I enjoyed the successes of the previous two seasons, so I must take ultimate responsibility for the disappointments of 2009.
“It has been a tremendous privilege to lead the Tigers on this amazing journey and I pay tribute to all the staff for their hard work and dedication as well as to the fans for their magnificent support. I am proud to have played my part and wish the club every success in the future.”