"I saw nothing, and I did nothing wrong," the former Democratic president said in an opening statement he shared on social media outside of the deposition.
The closed-door deposition in Chappaqua, New York, marks the first time a former president has been compelled to testify to Congress.
It came a day after Clinton's wife, former secretary of state Hillary Clinton, sat with Congress members for her own deposition.
Bill Clinton has also not been accused of any wrongdoing.
"Men — and women for that matter — of great power and great wealth from all across the world have been able to get away with a lot of heinous crimes and they haven't been held accountable and they have not even had to answer questions," said Republican James Comer, the chair of the House Oversight Committee, before the deposition began Friday.
Hillary Clinton told Congress members on Thursday that she had no knowledge of how Epstein had sexually abused underage girls and had no recollection of even meeting him.
But Bill Clinton will have to answer questions on a well-documented relationship with Epstein and his former girlfriend Ghislaine Maxwell, even if it was from the late 1990s and early 2000s.
Hillary Clinton said Thursday that she expected her husband to testify that he had no knowledge of Epstein's sexual abuse at the time they knew each other.
Republicans were relishing the opportunity to scrutinise the former Democratic president under oath.
"No one's accusing anyone of any wrongdoing, but I think the American people have a lot of questions," Comer said.
Republicans have wanted to question Bill Clinton about Epstein for years, especially as conspiracy theories arose following Epstein's 2019 suicide in a New York jail cell while he faced sex trafficking charges.
Those calls reached a fever pitch late last year when several photos of the former president surfaced in the Department of Justice's first release of case files on Epstein and Maxwell, a British socialite who was convicted of sex trafficking in December 2021 but maintains she's innocent.
Bill Clinton was photographed on a plane seated alongside a woman, whose face is redacted, with his arm around her.
Another photo showed Clinton and Maxwell in a pool with another person whose face was redacted.
Epstein also visited the White House several times during Clinton's presidency, and the pair later made several international trips together for their humanitarian work.
Comer claimed the committee has collected evidence that Epstein visited the White House 17 times and that Bill Clinton flew on Epstein's aeroplane 27 times.
In the lead-up to the deposition, Bill Clinton has insisted he had limited knowledge about Epstein and was unaware of any sexual abuse he committed.
"I think the chronology of the connection that he had with Epstein ended several years before anything about Epstein's criminal activities came to light," Hillary Clinton said at the conclusion of her deposition Thursday.
Comer has pledged extensive questioning of the former president.
He claimed that Hillary Clinton had repeatedly deferred questions about Epstein to her husband.
Democrats, who have supported the push to get answers from Bill Clinton, are arguing that it sets a precedent that should also apply to President Donald Trump, a Republican who had his own relationship with Epstein.
