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."
Former Netherlands international Wouters played 186 games and scored 21 goals during a six-year stint as a player with Utrecht, and previously had a spell as caretaker boss of the club in 1997.
Utrecht sit 11th in the Eredivisie with 38 points from 32 games.
