The school is a successor to the 'English Form' established in 1853, to educate local scholars.

The school is a member of the Headmasters' and Headmistresses' Conference (HMC).

Until 2020, John Lyon was an 11 to 18 senior independent HMC boys' day school in Harrow-on-the-Hill.

In 2020, John Lyon amalgamated with what was then called Quainton Hall Prep, located in central Harrow, to become an all-through School.

[5] The governing body of Harrow School retains some control of the John Lyon School; most responsibilities, however, are delegated to a John Lyon board of governors (officially styled Committee of Management).