The 24-year-old Fruean had open heart surgery in 2009 when he was first diagnosed with the illness, but his heart function had deteriorated over the last six months, the Crusaders said in a statement on Sunday.
"Robbie has been closely monitored over the past few months and in conjunction with his specialist team, the decision has been made to withdraw him from the remainder of the season and to have surgery," Crusaders doctor Deb Robinson said.
"While Robbie is facing major surgery he is otherwise fit and healthy which should stand him in good stead for his recovery."
The centre has been on the fringe of All Blacks selection over the last two or three seasons but never made the final step despite impressive form at the Super Rugby and provincial level.
Fruean was expected to spend about five days in hospital after surgery and begin gentle exercise about six weeks later, the Crusaders said.
The Crusaders are in fifth place in the standings on 51 points, five clear of the sixth-placed South African side Cheetahs and three behind Australia's Queensland Reds with a game in hand.
- Sports & Recreation
- open heart surgery