Wilnis started his career with the Sparta Rotterdam academy. After leaving the youth system at Sparta Rotterdam he joined NAC Breda in 1991. He spent four years at NAC Breda, making over one hundred appearances before joining De Graafschap in 1995. Wilnis also spent four years at De Graafschap and made over one hundred appearances for the club. In 1999, Wilnis joined English side Ipswich Town. He spent ten years at Ipswich, making over three hundred appearances for the club while also helping Ipswich win promotion to the Premier League in 2000. After leaving Ipswich in 2008, Wilnis joined Grays Athletic where he spent a single season. He retired from playing profesional football at the end of the 2008–09 season.