Armstrong and Travis Tygart met for six hours, according to a person with knowledge of the meeting who spoke on condition of anonymity because the discussion was meant to remain private.
The meeting, which was first reported by The New York Times, was the first between Armstrong and Tygart since late 2012.
The two have publicly sparred since the agency's investigation into doping by Armstrong and his US Postal Service team led to Armstrong's ban and his being stripped of his seven Tour de France titles.
Tygart has said that despite Armstrong's public confessions to performance-enhancing drugs use, he had to meet USADA to have any chance of reducing his ban, which covers sanctioned triathlons, marathons and other sports Armstrong enjoys.
Tygart did not immediately respond on Wednesday to a request for comment, while Armstrong's lawyer, Elliot Peters, declined comment.
The meeting with Tygart came after the March 8 release of the Cycling Independent Reform Commission (CIRC) report that seemed to question Armstrong's lifetime ban but stopped short of recommending it be reduced.
The CIRC report noted the "striking difference" between the lifetime ban on Armstrong and punishments of six months handed to other riders who were also caught cheating.
But it also noted that Armstrong deserved a "harsh sanction" and that some reduced penalties could be justified for riders who co-operated with USADA's initial investigation, which Armstrong did not.