The Patriots had been accused following the AFC championship game in January of intentionally deflating footballs (which many players say makes them easier to throw and catch). The incident was dubbed "deflategate" by some in the media. The league penalized Brady with a four-game suspension for the quarterback's actions and level of cooperation during the investigation.

An NFL spokesman told Reuters the league would not seek a stay for the judge's ruling pending appeal.

"The commissioner's responsibility to secure the competitive fairness of our game is a paramount principle, and the league and our 32 clubs will continue to pursue a path to that end. While the legal phase of this process continues, we look forward to focusing on football and the opening of the regular season," he concluded.

"We are grateful to Judge (Richard) Berman for hearing this matter, but respectfully disagree with today's decision," NFL Commissioner Roger Goodell wrote in the league's statement. "We will appeal today's ruling in order to uphold the collectively bargained responsibility to protect the integrity of the game.

The National Football League said Thursday that it plans to appeal a judge's ruling nullifying its four-game suspension of Brady related to the investigation into the possible intentional deflation of footballs last season.

New England Patriots Quarterback Tom Brady may have won a major victory, but the saga known as 'deflategate' isn't over yet.

Quarterback Tom Brady of the New England Patriots leaves federal court after contesting his four game suspension with the NFL on August 31, 2015 in New York City.

The decision from Berman said he voided the suspension in part because of "inadequate notice to Brady of both his potential discipline (four-game suspension) and his alleged misconduct."



The court also said it nullified the punishment because of "denial of the opportunity for Brady to examine one of two lead investigators"—NFL Executive Vice President and General Counsel Jeff Pash—and the "denial of equal access to investigative files, including witness interview notes."

The NFL denied Brady's appeal of the suspension in July, with Commissioner Roger Goodell charging that "important new information" helped firm up his decision.

Read MoreWhen the NFL doubled-down on its Brady suspension

"Notwithstanding my enormous respect for his accomplishments on the field and for his contributions and role in the community, I find that, with respect to the game balls used in the AFC Championship Game and the subsequent investigation, Mr. Brady engaged in conduct detrimental to the integrity of, and public confidence in, the game of professional football," Goodell wrote in July.



Drew Rosenhaus, sports agent and CEO of Rosenhaus Sports, said he would not advocate for getting the decision overturned if he were advising the league.

"If I were them I would move on. This has been a disaster for the NFL, they've gone after one of their icons—why I'm not sure—to an extent they've marred the season, it's been an overriding story this off-season, it's really had a negative impact on the Super Bowl," he told CNBC.

Read More 'Deflategate': Sales of Tom Brady merchandise double



"Now it's a terrible embarrassment, it's a huge victory for Brady and the NFL Players Association, and it's absolutely something that will set a precedent—in my opinion—for other players going forward," Rosenhaus added.



The Thursday decision could even potential affect the NFL going forward.

Rosenhaus said Goodell and his management are "big losers here and there's a lot of egg on their face," especially as there's been significant financial and time investment in punishing Brady.

Brady has denied any involvement in the footballs' deflation from the start. In a January press conference, the quarterback admitted that "every team is trying to do the best they can to win every week," but that he was "as surprised as anybody" about the allegations.



In response to the judge's ruling, the NFL Players Association said in a statement that the "decision should prove, once and for all, that our Collective Bargaining Agreement does not grant this Commissioner the authority to be unfair, arbitrary and misleading."

"While the CBA grants the person who occupies the position of Commissioner the ability to judiciously and fairly exercise the designated power of that position, the union did not agree to attempts to unfairly, illegally exercise that power, contrary to what the NFL has repeatedly and wrongfully claimed," the statement added. "We are happy for the victory of the rule of law for our players and our fans."