The FA council voted against the proposal in a meeting at its St George’s Park headquarters near Burton on Saturday and the decision could have far-reaching consequences.
Club owner Assem Allam, who first floated the idea in the summer of 2013, has threatened to sell the club should he not get his way.
Allam put the club up for sale after failing with his first application 15 months ago and it remains to be seen whether he will continue as owner.
A brief statement from the FA read: “The FA Council has rejected Hull City’s application to change their playing name to Hull Tigers.
“The council’s decision - carried by a 69.9 per cent vote of its members - came after a recommendation from the FA’s membership committee.
“The council, which is made up of representatives from across football, fully considered the recommendation in reaching its decision.”
The controversial plan to ditch the traditional Hull City AFC name in favour of Hull Tigers has been hugely divisive.
It was rejected by the FA council in April 2014, but the club won an appeal via an independent arbitration tribunal in March this year.
Allam then met an April 1 deadline to resubmit the case, but has again been frustrated.
The same three-man panel formed from the FA’s membership committee has reiterated its previous recommendation to reject the name change.
FA chairman Greg Dyke said that Hull would not be able to appeal this latest decision, but added there was nothing to stop the club reapplying to the governing body some time in the future.
He said: “That’s the decision. That’s what they have decided. Hull appealed the last one and that’s why it’s back here.
“I don’t think Hull can appeal. They could put in a new application to try to change it with better research etc and that might change the view, but as of now the Hull application has been rejected.
“It was an intelligent discussion and it was about two to one (against the proposal).”
Allam is convinced that rebranding the club is the only way to bring in new investment from overseas and his future with Hull is now in doubt.
Hull hinted that the club could be ready to continue the fight and insisted a name change was in their best interests.
A statement on Hull’s official website read: “The club acknowledges the FA council’s decision with regards to our name change application.
“We always knew that following a change to the FA’s policy the chances of changing the name were slim, but we also feel it is important to fight for what you believe in and we believe that being called Hull Tigers would be the best strategy for the future.
“We will be taking some time away from the club to consider our options and we will make no further comment until we have come to a conclusion.”
Discontent among the majority of Hull fans who oppose the name change and regular protests have been a feature of the club’s two-year stay in the Barclays Premier League before they were relegated last season.
Manager Steve Bruce has frequently been cast as mediator between supporters and owner.
He performed the role with aplomb, never compromising his popularity with the fan base but always underlining his respect for Allam.
Nearly two thirds of Hull City Official Supporters Club members were opposed to the name change in a poll carried out in April and May, with 459 out of the 704 who voted saying “no to Hull Tigers”.