On Twitter, McGowan addressed Maher directly, telling the host she remembered him allegedly talking about how big his "c--k" was.
"I was on your show Politically Incorrect in the late 90s- as the show returned from a commercial break, you leaned over to me & [sic] whispered in my hear, 'my parents didn't give me a good face, but they did give me a huge c--k,'" McGowan tweeted Saturday.
"I could feel your hot breath on my ear as an image of both your hideous face & alleged big c--k flashed in my mind. Both turned my stomach. I've always wondered what you say & do to the girls that aren't famous."
She added: "Bill, you got the face you deserved."
HBO did not immediately respond to Fox News' request for comment. Maher hasn't responded via Twitter either.
Maher hosted the talk show "Politically Incorrect" on Comedy Central before it moved to ABC -- airing between 1993 and 2002. He now hosts "Real Time with Bill Maher" on HBO.
McGowan's accusation came after an episode of Maher's show in which he discussed Tara Reade, the former U.S. Senate staffer who has accused former Vice President Joe Biden of sexual assault.
"What the f---?" Maher said on Friday's "Real Time." "We're letting this person [Reade] change the subject from Donald Trump, lethal incompetent, to Joe Biden, sex monster?"
Maher claimed that Republicans want Democrats to "go down the rabbit hole of 'Joe Biden, sex monster,'" insisting there was no "fact-finding here," regarding Reade's claims.
He described the Reade allegation as a case of "he said, she said -- she said something else entirely."
The HBO star appeared to dismiss Reade's recent assault claim by pointing to her past rhetoric, including when she said last year that she "wasn't scared of him, that he was going to take me in a room or anything, it wasn't that kind of vibe."
Fox News' Joseph A. Wulfsohn contributed to this report.