Scunthorpe's Gary Hooper scored twice as newly-promoted Stockport suffered their first league loss of the season.
The visitors led at the interval thanks to a well-taken goal from Hooper, who latched onto Grant McCann's pass before slotting home a low, angled shot.
And just after the break Paul Hayes' miscued shot fell invitingly for the alert Hooper, who lashed the ball into the roof of the net at the far post.
McCann sealed the win when he curled in free-kick from outside the penalty box.
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