"He tried to kiss me three times [in his office], so I rejected that, and when I rejected that, he asked me when my contract was up," Kelly, 45, said today on "Good Morning America." "As soon as I left his office, I called a lawyer, and I did bring the matter to a supervisor at Fox News."
"That person vouched for Roger's character, assured me that he was a good man, that he was likely just smitten and that I should try to avoid him, which I did," said Kelly, who said harassment from Ailes, 76, stopped after she avoided him for six months.
"He and I had gone on to have nine years of a healthy working relationship, and so in my mind I had attributed [it] to he was interested in me, he was having a marital difficulty, perhaps he was just interested in having an extramarital affair," Kelly said. "I wrestled with what to do because I wasn't sure what the truth was about Roger."
In September, Kelly's former Fox colleague Gretchen Carlson settled a sexual harassment lawsuit with 21st Century Fox in which Carlson alleged Ailes "sabotaged" her career after she "refused his sexual advances."
A source familiar with the deal told ABC News that the settlement was valued at $20 million. 21st Century Fox issued a public apology to Carlson, but Ailes has repeatedly denied allegations of sexual harassment.
Kelly said it would have been "a suicide mission" for her professionally if she publicly accused Ailes of harassment at the time she alleges it occurred.
"I now know the number of women who were targeted, and it's disturbing," she said. "But realistically, that would have been a suicide mission for me and my career."
She continued, "I wasn't Megyn Kelly of today. I had no power, and he was on the cover of industry magazines as the most powerful man in news. There was no one to go to."
Ailes denied the allegations made by Kelly in her memoir in a statement to ABC News sent by his lawyer, Susan Estrich.
Kelly said the things she said about Ailes in that Charlie Rose interview — that Ailes supported her professionally — are true.
"Both things can be true. A women can be harassed and then go on to have a good working relationship with the man harassing her," she said. "That is what happened in my case."
"What he said about promoting me and having my back over the next several years is true," she added. "It was one of the reasons even I found it hard to believe he was a serial harasser when the lawsuit broke and then women started coming forward anonymously."
Kelly said she believes Ailes would still be running Fox News if not for Carlson's lawsuit.
"We all had arbitration clauses in our deals, which prevented us from filing public lawsuits," said Kelly, who called 21st Century Fox Executive Chairman Lachlan Murdoch after Carlson's lawsuit to tell him of her own experience.
"What I wanted was for it to be an open and honest investigation into him. That's all I really wanted, because I didn't know whether it was just me or just Gretchen," Kelly said. "That's why I called Lachlan Murdoch to tell him — it didn't bring me any joy — but just to tell him that this did happen to me 10 years earlier and that they needed to take a hard look at who they had running the company.
"I cooperated with that investigation, and I think it wound up as it should have," she said.
Future at Fox News
Kelly said she is still figuring out whether to stay at Fox News as her contract comes up for renewal. She said she can "easily stay at Fox" but can also "go, hopefully, anywhere I want."
"I'm very grateful that Fox News has given me the 12 years I've had there and that they want me to stay," she said. "In my opinion the Murdochs, who are running Fox News Channel now, are honorable men who want to do what's right and who have a great vision for Fox News."
Kelly indicated she will do what is best for her family, which includes her three young children with her husband, Douglas Brunt.
"As much as I love my job, I love those three little lives that my husband and I have brought into the world," she said. "This is my philosophy, that I need to settle for more, so I'm going to do that."