The leader of the MLB Players Association is walking away ahead of what’s expected to be a contentious labor battle due to a federal investigation into allegations that he used licensing money to enrich himself.

Tony Clark, the union’s executive director, is resigning, The Post’s Joel Sherman confirmed, as the Eastern District of New York investigates allegations of misuse of licensing money.

Clark, 53, was set to begin his annual tour through spring training camps Tuesday at the Guardians’ facility in Goodyear, Ariz., but that was canceled.

An anonymous complaint filed with the National Labor Relations Board in 2024 alleged that Clark wrongly received equity in a licensing company the MLBA cofounded with the NFL players union in 2019 called OneTeam Partners, according to a June report by The Athletic. The MLBPA called the claim “baseless.”

That’s not the only controversy involving the union’s money matters.

ESPN reported in October that a Florida-based youth baseball company called Players Way, owned and created by the MLBPA, spent at least $3.9 million but held very few events for kids.

The union claimed it had put in the $3.9 million, but sources told ESPN the amount was closer to $10 million. And Players Way had narrowly cleared six figures in revenue.

New Mets second baseman Marcus Semien, one of eight members of the MLBPA subcommittee, said Tuesday he wasn’t “overly surprised” by Clark’s resignation due to the investigation.

The collective bargaining agreement expires Dec. 1.

“You definitely don’t want things to be a distraction going into December,” Semien said. “So that’s all I can really say, maybe (that is) why this is happening now.”

The owners’ desire for a salary cap — and the players’ insistence against one — will be at the forefront of CBA talks and could result in combative negotiations that many expect to impact the 2027 season.

This is a developing story. Check back for updates.