In 2006, Krauss helped organize a conference on gravity funded by a foundation run by Epstein. Krauss defended Epstein after his 2008 guilty plea of procuring for prostitution a girl below age 18. In 2011, Krauss told an interviewer, "As a scientist I always judge things on empirical evidence and he always has women ages 19 to 23 around him, but I've never seen anything else, so as a scientist, my presumption is that whatever the problems were I would believe him over other people...I don't feel tarnished in any way by my relationship with Jeffrey; I feel raised by it." In August 2025, The New York Times published reports of letters given to Epstein for his 63rd birthday, including one from Krauss. Krauss stated that he did not recall the letter but attended several gatherings at Epstein's home. In 2011, Krauss wrote to Epstein, "Beyond anything else, you are my friend. I hope we can both always remember that, no matter what." In an email dated 2017, Krauss asked Epstein for advice in responding to allegations of sexual misconduct.

“I sought out advice from essentially everyone I knew when false allegations about me were circulated.” He added that he had no knowledge of the “horrendous crimes” — the sex trafficking — that Epstein was later accused of. “I was as shocked as the rest of the world when he was arrested.”

In 2024, Krauss edited the book The War on Science, a collection of essays from 39 academics addressing perceived threats to academic freedom and scientific progress, such as DEI programs, wokeness, and cancel culture.