The College is named after Saint Elizabeth Ann Seton (1774-1821). Elizabeth established the first free Catholic school in America, from which began the present Catholic school system. She also founded the first Catholic orphanage and the first Catholic hospital. Canonised in 1975, she was the first American born saint.

The College was initially administered by the Daughters of Charity of Saint Vincent de Paul (1964-1994) for Brisbane Catholic Education. In 1995, the College appointed its first lay principal.