It was one of a number of 'free schools' created by James I in 1608 to provide an education to the sons of local merchants and farmers during the plantation of Ulster.

Although the school traces its origins to 1608, it experienced substantial challenges in its first three centuries of operation and was threatened with closure.

However, with the appointment of John Anderson as headmaster in 1924, and subsequently his son Douglas Anderson (1970-1989), then Ivan Bolton (1989-2009) and Edward Lindsay (2009-2020) the school has steadily improved with new facilities and a steady increase in enrolment.

[3][4] A few months prior to the reopening of schools following the COVID-19 lockdown it was confirmed that the school would be suspending its boarding policy indefinitely due to high cost and difficulty in maintaining social distancing measures, the first time this has happened in its over 400-year history.

In April 2022, it was announced that the Royal School would drop fees for the first time in its history given the lack of available funding from the department of education for fee paying schools.