In 1846, the Diocese of Killaloe lent its prestige and patronage to the private academy conducted at Springfield House, Ennis, by a Mr Fitzsimons.

In 1862, financial difficulties caused Fitzsimons to terminate his connection with Springfield, and under his successor the college changed direction sharply.

[citation needed] In 1865 the diocese broke with Springfield altogether and set up a diocesan college completely under its control at #12 Bindon Street, now a solicitor's office, and soon after became known as St. Flannan's Literary Institute, under a clerical headmaster, known for the first time as a president.

Work finally began in 1879 on land acquired on the Limerick Road, and the college was built to a rather severe neo-Gothic design.

Financial problems occasioned by the bankruptcy of the builder led to alterations in the plans, and some of the finishing touches were postponed, never to be completed.

During the Anglo-Irish War, the college was a hotbed of separatist sentiment, from where the Canon personally organised the collection of the famous Dáil Loan in Clare.

The early decades of the new state were grim as only limited funding was available for secondary education, and most costs had to be met out from the college's resources alone, but some curriculum development did take place.

The measure of the expansion that has taken place over the past thirty years is considerable; in 1962 there were some 370 pupils in St. Flannan's (140 of whom were day boys) and only 17 teachers.