The school was founded on 14 January 1861, on Mount St. Columba. The building has since went into other use as a retreat. A primary school, Holy Trinity, has been the school there since. Its original headmaster was Brother John Redmond. On its first day of activity one hundred and twenty boys, all aged between five and fifteen, showed up. In 1902 an extension, a second floor to the school and a third to the brothers' house, was added. This came at the time a considerable cost of £1,200 partly financed by an £800 loan from past pupils. Operations of the school were moved to old Church, Brook Street while construction was under way. Once finished the renovations provided the school with three more rooms; one for Manual Instruction, a sixty student accommodating classroom and a room with all the necessities for Practical and Experimental Science. The school moved to is present site on Kevlin Road in 1967. In 1993, after the resignation of Brother McCrohan, the school appointed its first non-clerical headmaster, Roddy Tierney, a former pupil of the school and a teacher in the school. At present the Principal is Mr. Foncy McConnell who was appointed Principal in March 2016, having being acting Principal for the previous year. At the time of appointment he was Vice Principal having taught in the school since 1987. Like Mr. Tierney he is also a former pupil of Omagh CBS.
Academics
The school's focus is academic, offering compulsory subjects of English Literature, English Language, Science, and Mathematics until GCSE. The School also focuses on the teachings of the Catholic faith, making Religious Studies compulsory at GCSE, and as a subsidiary weekly lesson during A Level years. In 2018, 94.2% of its entrants achieved five or more GCSEs at grades A* to C, including the core subjects English and Maths. In 2019 the school was ranked 18th out of 159 secondary schools in Northern Ireland with 86.7% of its A-level students who sat the exams in 2017/18 being awarded three A*-C grades.
Sports
In Gaelic football, the school has won the MacRory Cup in 1974, 2001, 2005 and 2007, and the All IrelandHogan Cup in 2007. and many other under-age level competitions for example Omagh CBS won the Rannafast Cup in 2009 and 2012 and the McCormick cup in 2008, 2009 and 2011
