U.S. District Court Judge Robert Doumar of Norfolk issued the ruling Monday against the National Marine Fisheries Service.
Commercial fishing representatives agreed with the ruling, but said it wouldn't give fishermen more flounder to catch this fall.
"We did not get much relief in terms of actual fish," said Jerry Schill, president of the North Carolina Fisheries Association. "However, had we not gotten the decision there's no telling what the NMFS might have done."
The fisheries association and the state of North Carolina asked the judge in March to again order the federal agency to publish the annual federal summer flounder quota within a reasonable period of time. That would allow fishermen to use the quota to plan their business.
"What good is a quota that meets the conservation goals of the fishery management plan if it is not announced until after the fishing season is over?" Doumar wrote.