The Portugal midfielder was one of a handful of United stars that spoke out against the plans in April.
United were one of 12 clubs to sign up to the proposals, which would have taken six Premier League clubs out of the national league and the Champions League to form a new cross-Europe competition.
The plans eventually collapsed after a huge backlash from supporters but the proposals are not dead in the water, with Real Madrid, Barcelona and Juventus remaining keen on salvaging the plans.
But United know they face the prospect of losing one of their star men should they try to revive their inclusion in any breakaway competition as the Athletic report that Fernandes was considering a departure from the club over their decision.
The 27-year-old was so furious with the club’s plans that he was willing to hand in a transfer request, as he felt the proposals went against what the club and the supporters stand for.
United’s executive vice-chairman, Ed Woodward, resigned in the aftermath of the collapse of the plans, though the club insist he had made the decision before that point.
Nevertheless, the club would likely face another backlash should they attempt to join another breakaway league proposal.
Supporters broke into Old Trafford on the day of United’s clash against Liverpool in May, forcing the game to be postponed.
Fans protested against the Super League plans, as well as the Glazers’ ownership of the club.
For more stories like this, check our sport page.