In 2011 Warrnambool College introduced a pastoral care system through six houses: Belfast, Childers, Flagstaff, Hopkins, Logans and Merri.

These houses are named after local colonial named landmarks in the region, including the Merri and Hopkins Rivers[3] Every year, a "celebration day" is held for each house, at different times of the year, in order to raise money for each house's charity, which are as follows: Hopkins: Francis Foundation[3] Merri: Loved and Shared[3] Childers: Warrnambool Coastcare Landcare Network[3] Belfast: Gillin Boys Foundation[3] Flagstaff: Leila Rose Foundation[3] Logans: Warrnambool & District Food Share[3] Warrnambool College hosts a campus of the Clontarf Football Academy for male indigenous students.

The Warrnambool College school colours are navy blue, white and green, as displayed in the school uniform The houses that all staff and students are placed in as part of the pastoral care program have the following colours: Belfast – Green Childers – Yellow Flagstaff – Red Hopkins – Blue Logans – Purple Merri – Orange In 2024, the school was brought before the Victorian Civil and Administrative Tribunal regarding student abuse towards teachers.

[4] VCAT has found that staff at the school at the time faced up to 20 violent and sexist attacks per day[5] and that 70 have been responsible for these incidents.

[4] The school has additionally been criticised for displaying quotes by certain far-right individuals.