Harris, who has been missing from Packers minicamp drills this week, underwent the procedure Tuesday at Bellin Hospital in Green Bay, agent Dave Lee told the Green Bay Post-Gazette.
"He's very thankful for regular checkups," Lee said. "Thankfully, the cyst wasn't cancerous. The interesting thing was he played with it last season, but they didn't find it until now."
Lee made the comments after Harris indicated on his Twitter account he had undergone the operation.
"EVERYTHING IS FINE, (doctors) found a fist sized cyst on my lung next to my heart. Shows the importance of getting routine check-ups, GET YOURS!" the 24-year-old running back wrote.
Packers Coach Mike McCarthy told reporters Harris will be out for the rest of the off-season but should be back in time for training camp.