The 39 year old had been in charge since December 2018, when he left his role as Wrexham boss to take the Shrews job.
"The club would like to place on record our thanks and acknowledge their hard work and dedication to STFC and the community and wish them all the best in the future.
"The search for a new manager will begin straight away and the club will aim to find the right candidate as soon as possible."
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