The 53-year-old was promoted to his current position in 2011, after previously serving as the assistant to previous incumbents Ton du Chatinier and Erwin Koeman.
Wouters guided Utrecht to a fifth-placed finish in the Eredivisie last season and a place in Europe.
However, the club were eliminated from the UEFA Europa League in the second qualifying round by Luxembourg minnows Differdange and have subsequently failed to match last season's standards.
Speaking to the club's official website, Wouters said: "I've been evaluating (the situation) and I think it's time for a new phase in my career.
"I want to experience the next step in my career. I can leave with a good feeling."
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