Stijnen moved from K.S.C. Hasselt to Club Brugge K.V. in 2000, aged 19, and became the club's first stand-in for veteran Dany Verlinden; when the latter retired at 41, he backed up Tomislav Butina.
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In 2006–07, Stijnen was between the posts as Brugge won the domestic cup (1–0 against Standard Liège), but the club only finished sixth in the league.