While CBC Perth was initially a day school, the rapid rise in population due to the goldrush saw the Brothers accepting boarders, with the first group welcomed in June 1896.

After a number of decades, accommodation became severely limited and the school was becoming overcrowded, so the search began for a larger property away from the city.

The Brothers looked at a number of different options and eventually settled on 254 acres of elevated land at the Mount Henry Peninsula on the Canning River. The new grounds, with 2kms of river frontage, were purchased from the Manning family for £9925.

Squads of boys from CBC Perth played a major role in clearing and preparing the site and in 1938 the boarders and some dayboys began moving to the new campus.

The Aquinas College foundation stone was laid on 11 July 1937 and when the school officially opened in February 1938, it had 160 boarders and 55 day pupils.

While CBC Perth continued to operate as a day school, Aquinas College inherited the College colours of red and black, membership of the PSA, as well as the College honour boards, achievements and history for the period 1894–1937. This was largely due to Brother Foley who was headmaster of CBC Perth at the time of the move and the founding headmaster of Aquinas College. Brother Foley was adamant that Aquinas College was not a new Christian Brothers school but an existing one that was simply evolving.

As a result, the colours of CBC Perth became blue, light blue and green, and the College raised new honour boards from 1938 onwards. In 1962 CBC Perth moved to a new campus by the Swan River on the East Perth foreshore and became Trinity College. This history is the reason Aquinas College and Trinity College have such a strong rivalry today.

In 1951, the College's premier oval, which overlooks the Swan River, was named Memorial Oval to commemorate Aquinians who lost their lives at war. A scoreboard was constructed on the oval and is named after Brother C. P. Foley.

The first new classroom block was built in 1955. It was named the 'Murphy Wing' in honour of Brother V. I. Murphy who was headmaster of the College from 1951 to 1956.

In 1975, Aquinas College became one of the first schools to have a 50-metre swimming pool. It coincided with the completion of the Redmond Learning Centre, which was named after Brother Redmond, a staff member at Aquinas College for over 45 years.