Allam's plans were met with vociferous protests by a section of the fans, and their hopes were boosted three weeks ago when the FA's membership committee said it would give a "unanimous recommendation" for the plan to be rejected.
A recent survey of season ticket holders fell on the side of Allam, with 2565 backing him compared to 2517 going against him. 9159 fans did not vote. But 63.5% of the FA council voted against the name change.
The saga has rumbled on in the background of Hull's successful season, which this weekend takes in an FA Cup semi-final against Sheffield United at Wembley.
A Hull statement read: "The club will not be making any comment on the outcome of today's FA meeting. Our focus is on supporting Steve Bruce and the team ahead of Sunday's FA Cup semi-final, our first in over 80 years. We look forward to seeing you all at Wembley."
Egyptian-born businessman Assem Allam bought Hull in December 2010 and announced plans late last year to change the club's name in a bid to raise its profile overseas.