In February 2003, Faber signed a new one-year contract extension with PSV. A month later, he had to rest for a few matches to rest his hamstring. In April, Faber broke his metacarpus in a match against De Graafschap. In May 2003, while playing with a cast due to his metacarpus injury, Faber suffered an inflammation of a bursa near his Achilles tendon. The injury required surgery and continued to provide problems in the 2003–04 season. He finally returned in the Champions League match against AS Monaco in November 2003, but received a hamstring injury during that game. He returned in an exhibition match against Trabzonspor in January 2004, but Faber suffered a new hamstring injury. He was sidelined for another month. On 22 April, the verdict from independent medical staff was that Faber could not continue his career. He announced his retirement, effective on that day. During his career, Faber underwent 13 surgeries for his injuries. In May, Faber was granted a fan farewell during the season's last home game.