Juncker, who will step down in the autumn after completing his five-year term, said he made a mistake by listening to British leader David Cameron when he told him to stay out of the campaign before the June 2016 vote.
"The then prime minister asked me not to interfere, not to intervene in the referendum campaign. It was a mistake not to intervene and not to interfere, because we would have been the only ones to destroy the lies that were circulated round," Juncker said.
"I was wrong to be silent at an important moment."
The former Luxembourg prime minister said it was one of two "major mistakes" he made during his mandate – the other being his slow response to the LuxLeaks financial scandal at the start of his term.
Britain's bombshell vote – by 52% to 48% – to leave the EU sent shockwaves through the bloc and came after a controversial campaign where both sides accused each other of peddling lies and exaggerations.
The process of actually leaving the EU has dragged on for nearly 3 years and is currently mired in bickering and infighting in the British parliament.
Cameron's beleaguered successor, Theresa May, has repeatedly failed to win approval for the deal she struck with Brussels, forcing the planned departure date to be put back from March 29 to October 31.