The team made the announcement Friday but did not provide specifics on when Malkin underwent the procedure or the nature of the surgery.
Malkin injured the knee in a collision against Boston on March 16. He missed seven weeks before returning to appear for the final four games of the regular season.
Malkin aggravated the injury before the first round of the playoffs. The Russian star sat out Games 1 and 2 against the New York Islanders but did have a goal and four assists in four games during Pittsburgh's first-round exit.
Malkin had eight goals and 20 assists in 33 games for the Penguins, who won the East Division title. The four-time All-Star and 2012 Hart Trophy winner turns 35 in July and is entering the final year of his contract.