Pettitte, a longtime close friend of the ex-baseball great, told a Washington jury his former Yankees teammate made the admission to him in 1999 or 2000, The New York Times reported.
Pettitte, a 13-year member of the Yankees who is now attempting a comeback, testified that Clemens accused him in 2005 of remembering the conversation inaccurately, the newspaper said.
Clemens since insisted he had been talking about his wife, not himself.
"Obviously, I was a little flustered because I thought that he had told me he did," Pettitte said of Clemens' alleged HGH use. "My reaction after that was, well, no good asking him or talking to him about this now, and I just walked out, end of the conversation."
Pettitte has previously admitted using HGH, which has since been banned from the game as a performance-enhancing drug.
Clemens is accused of lying under oath to a congressional committee investigating performance enhancing drugs in baseball during 2008 testimony. Prosecutors say he falsely denied using the drugs.