Duffen resigned his position on Thursday morning following continued speculation over his own future and that of Tigers manager Phil Brown.
His statement 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 unchartered 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. But 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."
Pearson has been strongly linked with a return to the KC Stadium after he opted to leave Championship club Derby on Wednesday, with Hull revealing a further statement will be made on Monday, November 2 regarding the appointment of a new executive chairman.