Crewe had been interested in a permanent deal for the 20-year-old, while several Championship clubs, including Leeds United, were understood to have been keen.
"This is a great opportunity for me and I will do my best to take it as soon as possible," Aneke told Zulte's official website.
"I think Belgian football will suit my playing style.
"Zulte Waregem give opportunities to young players and this club, after some good conversations, was a logical choice for my future development."
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