He is expected to be sidelined four to six weeks.
Pippen, who underwent a similar procedure last March, has missed eight of the team's first 20 games this season, all but one due to soreness and swelling in the knee.
The 38-year-old forward signed a two-year, $10.3 million contract with Chicago during the summer, returning to the city where he and Michael Jordan won six championships in the 1990s. But having to undergo another operation has him contemplating retirement.
"I question myself whether or not I can play another year," Pippen said before the surgery. "I just have to wait and see."