In 1863, the school was renamed "St Boniface Boys' Catholic School" and relocated to a larger building to Melbourne Street, and later to North Road with Mr Clarke as Head Master. From the beginning both boarders and day boys were catered for.
Mr Clarke resigned his post in 1883, but in September of the same year the Basilian Fathers, exiled from France, bought over the property at Beaconfield, Plymouth. This was at the time a considerable distance from the city's residential area and the efficient transport system of today did not exist. Hence, whilst the boarders were accommodated at the residence at Beaconfield a small school for day boys was opened at Grosvenor Street near the centre of Plymouth. It was known as the Catholic Institute and was staffed by teachers from Beaconfield. Mr Clarke who apparently could not suppress his vocation to teach, again took over the school at Grosvenor Street and a little later transferred the pupils to his own residence at Wyndham Square where he carried on his valuable work until 1891. The boarding school at Beaconfield continued under the management of the Basilian Fathers until July 1899, when, under the stress of financial difficulties, they resolved to close the school.
The following year the diocesan authorities purchased premised at Wyndham Square, and the school was placed under the patronage of St Boniface. It was staffed by the diocesan clergy under the headmastership of Provost Burns.
The De La Salle Brothers were invited to take over the management of the school in 1911, but on the outbreak of World War I were recalled to France. Their places were taken by the Presentation Brothers who found the premises at Wyndham Square inadequate, and gave up in 1931.
In September of that year the College accepted an invitation of Barrett to re-open the school at Beaconfield. The buildings had been erected in 1910 as a convent boarding school, provided excellent accommodation for the 127 day boys and fifteen boarders who opened a new era in the schools chequered career.
With the outbreak of World War II the College was evacuated to Buckfast Abbey between 1941 and 1945. The Abbey was instrumental in assuring the school continued during those difficult war years. During this period, the school buildings in Plymouth were used as strategic operation bases for the Admiralty and continued to be used even after the students returned to Beacon Park.
In 1946 the College was encouraged to become one of the 179 direct grant schools where fees for selected day pupils from lower income families were partly or fully paid by the local authority. The College retained autonomy from the local authority and remained members of the Headmasters' Conference. Situated in Beacon Park, it had 450 boys in the 1970s.
When the Labour Government withdrew funding from direct grant schools in 1976, the College, like Manchester Grammar School and others, was forced to decide between reverting to a fully independent school or becoming a Voluntary-Aided school. After a period as an independent school, in 1981 St Boniface’s Catholic College and Bishop Vaughan Catholic School were amalgamated into a Voluntary-Aided boys’ Comprehensive school at Crownhill, which then became the Grant Maintained St Boniface’s Catholic College. Notre Dame High School became a state school at the same time. In 1999 the College reverted to Voluntary Aided status. On January 1, 2008 the College was renamed and readdressed as "St Boniface's Catholic College" at 21 Boniface Lane, Manadon Park, Plymouth.
Today the College is a five-form entry college of 813 students between the ages of 11 to 18, taught by a full-time staff of 50. Its main campus is at Manadon Park with sports facilities at Marsh Mills and Manadon Astroturf. Its sister school is Notre Dame Catholic School. It is colloquially known as "Bonnies" or abbreviated as SBCC.