The lawyer and business executive said in a statement that he did not create the account that appears on the site.
"I am certain that the account in question is not mine," Biden said in a statement provided to CNN. "This account was clearly set up by someone else without my knowledge and I first learned about the account in question from the media."
The existence of the account was first reported Monday by Breitbart News
, which found the account information in searching through the huge trove of data on the site's users that was dumped online by hackers earlier this month.
The conservative website reported that the account was registered to a Robert Biden in Washington, D.C., though the date of birth is off by 10 years.
Biden's full name is Robert Hunter Biden.
The account was from an "attached male" who was apparently seeking "anything goes." It was created in 2014.
In his statement, Biden said he stopped using the email address that was used to set up the account because he believed it may have been compromised, and alluded to other times he was impersonated in an attempt to sully his reputation, though he did not name any specific incidents.
He also cited press reports that the website did not verify emails used to create accounts -- meaning that theoretically anyone can register with an email address even if they do not control the address.
"I am certain that is what happened in this case," Biden said.
Biden is the younger of the vice president's sons. His older brother, Beau Biden, died of brain cancer earlier this year.
Hunter Biden, an investment banking executive and lawyer, is also no stranger to uncomfortable headlines. Last year, he was discharged from the Naval Reserve after testing positive for cocaine.
The hack of Ashley Madison dumped account information of more than 30 million users online. The site caters to married people looking to have affairs.