In 1996, Faber won his second Super Cup after defeating Ajax with 3–0. But in September, Faber tore his ankle ligaments after attempting a headed duel with Utrecht’s John van Loen. It turned out to be the first of a long line of injuries that would dominate Faber’s career. Cartilage was removed from Faber’s ankle, sidelining him for a long period. He would play only nine Eredivisie matches in the 1996–97 season, the year that PSV won the league. In the 1997–98 season, Faber played three matches before suffering an achilles tendon injury. He recovered in time for a training camp in Spain, but it was there when he noticed the injury did not completely heal yet. That year, Faber appeared in 21 league games and scored twice. In February, he was sent off in a match against Ajax. In May, Faber tore his right Achilles tendon in a match against Groningen. The injury was called "career threatening" by the PSV club doctor and forced Faber to recover for months, therefore missing out on a possible World Cup participation.