Johnstone, 18, was drafted in to the club in August after an injury to first-choice Iron keeper Josh Lillis.
He made 12 appearances for the club, keeping two clean sheets.
Although Lillis is not yet ready to return from his knee injury, he faces a fight to get the gloves back off Sam Slocombe - who was preferred in Saturday's 2-1 win at Hartlepool and has featured in 12 games this season.
Johnstone, writing on Twitter said: "[I] enjoyed my time at Scunthorpe. I'll keep a luck out for Scunthorpe results."