The RCO was founded as the College of Organists in 1864 by Richard Limpus, the organist of St Michael, Cornhill, in the City of London, and received its Royal Charter in 1893. In 1903 it was offered a 99-year lease at peppercorn rent on a building designed by the architect H. H. Cole in Kensington Gore, west London. When it became clear in the mid-1980s that an economic rent would be charged on expiry of that lease, the lease was sold and the college moved into new accommodation in 1991. The building subsequently become the home of property tycoon Robert Tchenguiz.
In 2003 plans were announced for more permanent purpose-built premises around the Grade I listed former Curzon Street railway station in Birmingham, a notable piece of monumental railway architecture. New facilities designed by Associated Architects included a new library and 270-seat concert hall. However, in 2005 the RCO announced that this move would not be taking place and subsequently that it would no longer be looking for a permanent home of this kind, focusing instead on activities such as education, events, examinations and member services.
In 2014 the college celebrated its 150th anniversary with a year-long programme of events including recitals, conferences, music festivals, courses and publications. In 2020 the RCO announced that Saturday 18 April would be its inaugural National Organ Day.
In July 2023 the College announced that the conductor and organist Sarah MacDonald had been elected as its President, taking office in July 2024.
In 2024 King Charles III accepted the patronage of the RCO, succeeding his mother, Queen Elizabeth II, after her death in 2022.
Throughout 2025 the College ran "Play the Organ Year 2025", a national initiative created with partner organizations to encourage people to take up the organ and to introduce wider audiences to organ music through "First Encounter" recitals, hands-on playing sessions and online resources. The organist Anna Lapwood served as its patron.
On 8 March 2025 the College presented its RCO Medal at Southwark Cathedral to the recording producer Gary Cole, the choral conductor Sofi Jeannin and the composer Cecilia McDowall, recognizing distinguished achievement in organ and choral recording, choral directing and composition respectively.
In 2025 the College introduced a new suite of Diplomas in Choral Directing, establishing a progressive pathway of Colleague (CChD), Associate (AChD) and Fellowship (FChD) qualifications alongside its long-established organ-playing diplomas. Regulations for the Associate diploma were scheduled to be published in autumn 2026 and those for the Fellowship diploma in early 2027.