Henry was forced to withdraw from his country's team to face South Africa earlier this month and subsequent tests revealed he had suffered a temporary blockage of a small blood vessel in his brain.
However, the Ireland Rugby Football Union (IRFU) confirmed on Tuesday that further investigations had uncovered a defect in the Ulster player's heart wall, which was duly operated on.
"Chris is recovering from a procedure yesterday to repair a defect in his heart wall," read the statement.
"This was found to be related to his recent episode and has been performed to prevent further issues."
Ulster remain hopeful that the 30-year-old can return to the professional game.
Chief executive Shane Logan was quoted by BBC Sport as saying: "I think we'd be optimistic that he will make a full recovery and come back as quickly as possible."
Ireland are not in action again until February when they begin their Six Nations campaign with a trip to Rome to face Italy.