On July 6, 2016, former Fox News anchor Gretchen Carlson filed a sexual harassment lawsuit against Ailes; Carlson's allegation were the impetus for more than a dozen female employees at 21st Century Fox to step forward regarding their own experiences with Ailes’ behaviour. Carlson alleged that she had been fired for rebuffing Ailes' advances. Ailes, through his attorney, Susan Estrich, denied the charges. Three days later, Gabriel Sherman reported accounts from six women (two publicly and four anonymously) who alleged sexual harassment by Ailes. In response, Ailes' counsel released a statement: "It has become obvious that Ms. Carlson and her lawyer are desperately attempting to litigate this in the press because they have no legal case to argue. The latest allegations, all 30 to 50 years old, are false."
On July 21, 2016, Ailes resigned from Fox News, receiving $40 million from 21st Century Fox (the then-parent company of 20th Century Fox and Fox News) in an exit agreement. Rupert Murdoch succeeded him as chairman, and as interim CEO until the naming of a permanent replacement. In a letter to Murdoch, Ailes wrote: "I will not allow my presence to become a distraction from the work that must be done every day to ensure that Fox News and Fox Business continue to lead our industry." Ailes was thanked for his work, without mention of the allegations. He continued to advise Murdoch and 21st Century Fox through 2017 until his death.
Following Ailes's resignation, Andrea Tantaros claimed in August 2016 that she approached Fox News executives about Ailes's behavior towards her in 2015. She stated that her allegations resulted first in her being demoted, and then in her being taken off the air in April 2016. Tantaros filed a lawsuit against Fox News in August 2016 for sexual harassment, also accusing Bill O'Reilly and Scott Brown.
On August 8, 2016, Shelley Ross, writing for The Daily Beast, described her encounter of sexual harassment with Ailes in 1981. She claimed that at a lunch meeting Ailes asked her, "When did you first discover you were sexy?" When Ross explained to Ailes that she found the conversation "very embarrassing," he responded that "the best expression of loyalty comes in the form of a sexual alliance." The next month, 21st Century Fox announced it had settled a lawsuit with Carlson over her allegations of harassment against Ailes. 21st Century Fox was also reported to have made separate settlements with at least two other women who made complaints about Ailes.
In November 2016, Fox News anchor Megyn Kelly wrote in her book about the details of her sexual abuse allegations against Ailes. According to Kelly, when she first joined Fox News, Ailes would have meetings with her, during which he would make sexual remarks. Kelly alleges that he also tried to kiss her several times during a closed-door meeting, but she was able to get away and leave the office. After that incident in 2006, Kelly says that Ailes did not sexually harass her again. Then, in 2016, when Gretchen Carlson first made her sexual abuse allegations, 21st Century Fox pressured Kelly to defend Ailes, which she refused to do.
In 2016, after he left Fox News, he became an adviser to the Donald Trump campaign, where he assisted with debate preparation.