Citing friends of the couple, the article also claimed that Mrs Trump pushed her husband to run for the White House because she knew he would be unhappy if he didn’t.
Mrs Trump has faced repeated suggestions that she was a reluctant first lady since her husband Donald Trump was elected just over a year ago.
In revealing conversations with those who know the couple well Vanity Fair was told that Mrs Trump had “never been too crazy” about a presidential run, but had emerged as the person with “most control” over her husband in the White House.
One long time friend of the 47-year-old Slovenian-born former model told Vanity Fair: “This isn’t something she wanted and it isn’t something he ever thought he’d win.
“She didn’t want this come hell or high water. I don’t think she thought it was going to happen.”
A spokesman for the first lady slammed the “salacious” report and said Mrs Trump was “honoured” by her role.
“Once again part of the liberal media, this time Vanity Fair, has written a story riddled with unnamed sources and false assertions,” Stephanie Grisham, the first lady’s communications director, said.
“As a magazine tailored to women it is shameful that they continue to write salacious and false stories meant to demean Mrs Trump, rather than focus on her positive work as First Lady as a supportive wife and mother.”
Following Mr Trump’s victory in November 2016 Mrs Trump, the president’s third wife, stayed in New York with their 11-year-old son Barron before moving to Washington the following summer.
But Roger Stone, a veteran Republican strategist and early adviser to Mr Trump’s campaign, told the magazine it was Mrs Trump who had pushed the businessman to stop prevaricating and make the decision to run.
Mr Stone said: “She was very clearly the one who said ‘Either run or don’t run’. She knew it was in his blood, he always wanted to run. She is the one who pushed him to run just by saying ‘run or do not run’.
“I don’t think she was ever too crazy about it. She said ‘It’s not my thing, it’s Donald’s thing’. I think she understood he was going to be unhappy if he didn’t run.”
Despite her reluctance Mrs Trump has emerged as a more popular figure than her husband. In a recent poll 44 per cent of Americans viewed her favourably, while Mr Trump had an approval rating of 41 per cent.
Ivanka Trump, the first daughter, was also less popular than Mrs Trump with a 41 per cent rating, the same as her father’s.
In September Mrs Trump launched her long awaited anti-bullying campaign and some friends said she was growing into her role.
Tom Barrack, the billionaire investor and long-time friend of Mr Trump, told Vanity Fair: “The one who has the most control over Donald is Melania, 100 percent, and he listens to her and adores her.”
Paolo Zampolli, a former modeling agency boss who introduced the couple and is now a US ambassador, said of Mrs Trump: “She knows what she wants.”
At the weekend Ivana Trump, the president’s first wife, told a radio show she thought the president himself was missing the life he had previously led.
She said: “I think he’s missing a little bit of his old life. You know he was in Trump Tower, and he would go to Mar-a-Lago, he would go to play golf on Westchester, and things like that.”