After progressing through the Genk youth system, Courtois, aged 16 years and 341 days, made his first team début for Genk on 17 April 2009 against Gent. He was a key figure in Genk's title victory in the 2010–11 season in the Belgian Pro League whilst living in Belgium. He received the Goalkeeper of the Year and Genk's Player of the Year award, only conceding 32 goals over the course of 40 league matches and keeping 14 clean sheets for Genk.