The 25-year-old was expected by many to leave St Mirren Park when his contract expired this summer with several English clubs reportedly interested in signing the former Celtic midfielder.
However, McGowan, who has scored 21 times in 115 appearances for the Buddies, will be part of Danny Lennon's plans until 2014.
The Paisley club also confirmed that keeper Grant Adam has cancelled his contract by mutual consent.
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- Danny Lennon