Bolton School is one of the oldest schools in Lancashire. The origins of the Boys' School can be traced back to at least 1516 when the Bolton Grammar School for Boys was recorded as being "a going concern". In 1644 it was endowed by Robert Lever and so began a long and close relationship with the Lever name.

The Bolton Girls' Day School was established in 1877 and was one of the earliest public day schools for girls in the country. It was quickly renamed to Bolton High School for Girls and moved to the Park Road site (where the current Junior Boys' School stands) in 1891, where it was opened by the suffragist Mrs Millicent Fawcett with 67 girls.

In 1913 Sir William Hesketh Lever, the first Viscount Leverhulme, gave a generous joint endowment to the High School for Girls and the Bolton Grammar School for Boys on condition that the two should be equal partners known as Bolton School (Boys' and Girls' Divisions). On 1 April 1915, the Bolton School Foundation formally came into existence.

William Lever's vision included the building of a new school, with one wing for boys and one for girls. War delayed the construction and it did not begin until 1924: it was only fully completed in 1965.

The School recently celebrated its long history with a year of Centenary activities in 2015, 100 years after the School was re-endowed, and 500th anniversary celebrations in 2016.