His younger brother Ogbonna told BBC Sport that the former Arsenal striker is doing well after the operation.
"It's important to clarify that decision to operate him was reached during his annual medical check-up.
"We give thanks to God that everything went well and he's in perfect condition.
The decision to operate him was reached during his annual medical check-up
"The family would like to say a big 'thank you' to Nigerians and Nwankwo Kanu's fans across the world for their prayers and best wishes."
The former Nigeria captain first had heart surgery in November 1996 to correct a faulty aortic valve.
After year out, he returned to action for Inter Milan and in February 1999 joined Premier League side Arsenal.
The experience prompted him to set up a foundation to build five hospitals in Africa to treat undiagnosed heart disease and provide surgery.
At the weekend, the Nigerian government named Kanu among the 100 most distinguished Nigerians during a ceremony to mark the centenary of the unification of north and south Nigeria.
Kanu announced his retirement from international football at the 2010 World Cup in South Africa.
His international success includes a Fifa under-17 World Cup title in 1993 and the 1996 Olympic football gold medal.
Kanu's individual honours include African Footballer of the Year awards in 1996 and 1999.
Nwankwo Kanu is recovering in the United States after undergoing corrective heart surgery.