Alflen had been part of Wouters' backroom staff at the club in recent seasons and has been promoted from his role as assistant coach, signing a one-year deal.
The 46-year-old spent six years at Utrecht as a player and the link between the two parties has seen him given his first head-coach role, leaving the former Ajax midfielder looking forward to a new challenge.
"My first job as a head coach in professional football, in the city where I live, at the club where I was allowed to make my debut as a young player and I've previously held various positions; I look forward to it," Alflen told Utrecht's official website.
Alflen will work with recently appointed technical director Co Adriaanse, and the new head coach hopes to learn from the former Twente boss next season.
"In my conversations with Co we share a vision for the style of play and the intentions of a team," he added.
"I look forward to working with Co and to fulfil the ambitions of FC Utrecht."
Utrecht finished 10th in the Eredivisie this season, six points off qualifying for the UEFA Europa League play-offs.
