The move comes less than a year after the former Sydney FC product joined Schalke from NPL NSW side Sydney Olympic.
The 21-year-old central defender enjoyed a successful season with the Bundesliga club's U-23 side earning a call up to the first team.
In May the Canberra product was given his Bundesliga debut during Schalke's win against Stuttgart after impressing manager Huub Stevens with his performances in training.
Timotheou was also named on the bench for Schalke's in four other matches but did not see any game time.
His new club Zulte-Waragem are a three time champion of Belgium's top league but finished last season 11th of sixteen teams.
He will be one of two Australians playing in Belgium next season alongside Danny Vukovic who plays at reigning league Champions KRC Genk.
Timotheou could make his debut for Zulte on July 28 when they play KV Mechelen.