In 1996, Ajax sold Kanu to Serie A side Inter Milan for around $4.7 million. That summer he captained the Nigeria national team that won gold at the Olympics, and scored two late goals in the semi-finals against powerhouses Brazil to overturn a 2–3 scoreline into a 4–3 win in extra time.

However, soon after returning from the Olympics, Kanu underwent a medical examination at Inter, which revealed a serious heart defect, and it was believed by doctors that his career was over. He underwent successful surgery in November to replace an aortic valve, and did not return to his club until April 1997.