The school was formed in September 2009 from the merger of Withins School and Top o'th' Brow Primary School, both community schools administered by Bolton Metropolitan Borough Council. Bolton St Catherine's Academy became part of The Bishop Fraser Trust in May 2018 alongside Canon Slade School and St James's CofE High School.[2] It coordinates with Bolton Council for admissions. The school offers Nursery, primary - double class entry per year, secondary - 160 per year, education for pupils aged 3 to 16.
In 2012 Bolton St Catherine's Academy relocated from the two former school sites to a new campus on Stitch-Mi-Lane. The new campus also houses Firwood Special School, a community special school for pupils aged 11 – 16.