The FEC’s decision came three years after a complaint on the $150,000 payment was made by nonprofit government watchdog group Common Cause.
It had claimed that the payment was an illegal, in-kind contribution made to the one-term president’s election campaign.
But the FEC’s six-member commission did not find Mr Trump or his campaign violating election laws.
Common Cause was told of the decision on Tuesday, but the FEC has 30 days to release more details on its decision.
Ms McDougal, who was paid the money in August 2016, later told The New Yorker that she had an affair with Mr Trump in 2006 and 2007.
Mr Trump has strongly denied the allegation.
He served more than a year in prison for federal campaign finance violations, as well as other crimes.
The FEC has already dropped an investigation into whether Mr Trump violated election laws when Mr Cohen paid Ms Daniels $130,000 before the 2016 election.
Ms McDougal later sued AMI, which was run by Mr Trump’s friend David Pecker, claiming they had bought her story and deliberately not published it to prevent embarrassing Mr Trump as he tried to win the White House.
AMI, which is now known as AM360, agreed to “not to contest” that the payment to Ms McDougal, “combined with its decision not to publish the story, in consultation with an agent of Donald J Trump and for the purpose of influencing the election, constituted a prohibited corporate in-kind contribution.”
The agreement was reportedly signed last month but only made public on Tuesday.
As part of the agreement, AM360 reportedly acknowledged the FEC’s findings but said it did not knowingly or wittingly violate the law.