FFA CEO Ben Buckley said he had advised the leader of the NQFC bid, Don Matheson, of the decision today.
"The decision follows a competitive process involving two applications for a Hyundai A-League license in Townsville," Buckley said.
"The level of interest in the Townsville region reflects the momentum behind the growth and development of the Hyundai A-League, as well as the strength of the North Queensland region."
Buckley said that NQFC has one month to finalise its submission to FFA.
"Queenslanders have enormous pride and spirit in their sporting teams.
"I hope the potential to have a team of their own in the Hyundai A-League will inspire all North Queenslanders to be part of this exciting opportunity.
"Participation in the Hyundai A-League not only gives North Queensland another presence in a national sporting competition but also the potential to represent the region through Asian competition."
Buckley expressed his appreciation to the other consortium, led by Melbourne businesswoman Milissa Fischer, for her interest in the Townsville license also.
"We are very encouraged by the level of interest in the Hyundai A-League," Buckley said.
"Since it commenced three years ago, it has had 'cut through' in the busy Australian sporting landscape with average crowds, viewership, membership, media coverage and profitability trending upwards each season.
"The attractiveness of the competition is clearly reflected in the level of interest in our expansion plans."
FFA's view is that the Hyundai A-League has the capacity to be at least a 12 team competition.
"When and where we expand the competition is measured simply by whether it is right for football, right for the existing Hyundai A-League clubs, right for the new clubs and right for the local community," Buckley said.
"In the meantime, we look forward to NQFC entering the competition in 2009."