The school first opened its doors in January 1958 as Burscough County Secondary School under the headship of Brian Stone. His staff of just 10 teachers looked after the 222 pupils on roll at that time. The official opening of the school took place some 6 months later on the 10th June 1958 when the then Edward John, 18th Earl of Derby (1918 – 1994) presided over the ceremony.
The school motto E PLURIBUS UNUM, (Out of Many, One), which is also the motto of the USA, was thought to be appropriate as the new school was created from several all-age schools from around the area. The school was extended in 1976 and became Burscough Priory High School. During this time the roll expanded to over 800 pupils with the comprehensive intake. Brain Stone retired in July 1984 and Eric Cole took on the role of acting Headteacher for the Autumn term in 1984 until the appointment of Roger Leighton as headteacher in January 1985.
In September 2004 the school once again changed its name to become Burscough Priory Science College to reflect the gaining of specialist school status in Science. The new science and performing arts building was handed over in the same month and was officially opened on 25th May 2005 and named The Brian Stone Centre. Mr Leighton retired in August 2009 and was succeeded by Mr D Bruce, who had previously served as a Deputy Headteacher at Burscough Priory. Mr Bruce left Priory in Spring 2011 having overseen the development of the school’s new ECM Centre. The school was under the headship of Catherine Davies and later Graham Clarke through the period 2012-2018.
In September 2018, the school joined Endeavour Learning Trust and was officially renamed as Burscough Priory Academy, under the executive headship of Lesley Gwinnett.