The 54-year-old British actress spoke about the affair for the first time -- 20 years later -- in Britain's Sunday Times magazine saying that it was all "blood under the bridge."
"You can't hold on to anything like that," Thompson said. "I just think ... pfft. It's pointless. I haven't got the energy for it. Helena and I made our peace years and years ago."
The "Saving Mr. Banks" star married Branagh in 1989 but their marriage came to a seemingly amicable conclusion in 1995 because of work priorities keeping them apart; however, speculation of infidelity made its way into the tabloids.
Carter and Branagh had been linked for five years starting in 1994 when she played his love interest in his take on "Mary Shelley's Frankenstein."
Thompson, however, went into a state of depression when her marriage ended that continued for some time.
The Oscar-winning actress said that she worked those feelings into her role in the 2003 film "Love Actually," when she played Alan Rickman's cheated-on wife.
"I've had so much bloody practice at crying in a bedroom, then having to go out and be cheerful, gathering up the pieces of my heart and putting them in a drawer," she said.
But she also said that she understood why Branagh may have been interested in Carter, whom she sees as similar to herself "being slightly mad and a bit fashion-challenged."
"Perhaps that's why Ken loved us both. She's a wonderful woman, Helena," she added.
Both actresses appeared in the blockbuster "Harry Potter" franchise, which eventually became a who's who of British talent. Branagh appeared in the second of the eight films, which did not star either of the actresses.
Thompson went on to marry Greg Wise about a decade ago and the couple have two children together, Gaia, 13, and a former Rwandan child solider named Tindyebwa Agaba, 26, who Thompson adopted when he was 16.
In 2005, Branagh married film art director Lindsay Brunnock. Carter has been linked to director Tim Burton since 2001 and the couple have two children together.
In 2002, Carter took aim at the press who painted her as "a habitual, serial home breaker" soon after she started dating Burton, who had just split with model/actress Lisa Marie Smith.
"It gets frustrating because I know the story and the truth of it," she said (via the Daily Mail.) "It is very hurtful and, frankly, some of the things I have been called are quite libelous. But it's part of the price of being in the public eye."
