Speaking on Tuesday night to Joan Tarshis, one of several women who recently accused comedian Bill Cosby of rape, the anchor asked whether she had considered biting Cosby's penis when he allegedly forced oral sex on her.
The question left Tarshis somewhat confused and sparked a major backlash against the anchor.
On Wednesday, Lemon took to the air to apologize.
"As I am a victim myself, I would never want to suggest that any victim could have prevented a rape," Lemon said.
"If my question to her struck anyone as offensive, I am sorry, as that certainly was not my intention," he added.
Lemon previously identified himself as a victim of a pedophile during a broadcast in September 2010.
Interviewing congregants of Georgia pastor Eddie Long, who faced accusations of pedophilia, Lemon said he was victimized as a child.
"I've never admitted this on television. I was a victim of a pedophile when I was a kid, someone who was much older than me," Lemon said.
Watch the clip, via Media Matters: