Matthews has always been known to have a combative relationship with former candidate Clinton.
"Where's that Bill Cosby pill I brought with me?" he asked. Matthews then laughs, delighted with the line, for an extended moment, as the staffers around him react with disbelief, clearly uncomfortable.
Matthews responded to the newly discovered clip, telling NY magazine on Friday that it "was a awful comment I made in poor taste during the height of the Bill Cosby headlines", adding, "I realize that's no excuse". He said, "I deeply regret it and I'm sorry".
Reps for Clinton didn't immediately respond to a request for comment from TheWrap.
A fast-talking political junkie, Matthews has served as the host of "Hardball", a fixture on MSNBC's programming lineup, since 1997. He once pinched her cheek after an interview, and, in 2008 said, "the reason she's a USA senator, the reason she's a candidate for president, the reason she may be a front-runner is her husband messed around".
In 2016, following a primary victory by then-candidate Donald Trump, Matthews was caught on mic fawning over Melania Trump as she was shown on screen.
The MSNBC spokesman said that they thoroughly reviewed the situation at the time and that Matthews received a formal reprimand.