Befriended Epstein after Epstein's 2008 conviction and remained in touch with him at least through 2017. Chomsky considered Epstein a "highly valued friend and regular source of intellectual exchange and stimulation". Congress released a photo of Chomsky with Steve Bannon from Epstein's estate and another showing him flying with Epstein in Epstein's private plane. Chomsky said he received around $270,000 from an account connected to Epstein.

In 2026, Valeria Chomsky wrote that Chomsky's relationship with Epstein was a "grave mistake" and apologized on Chomsky's behalf, writing, "It was deeply disturbing for both of us to realize we had engaged with someone who presented as a helpful friend but led a hidden life of criminal, inhumane, and perverted acts."

In 2023, Chomsky suffered a massive stroke. He can no longer walk or communicate.