St Aloysius Pre-University College is a sister concern of Mangalore Jesuit Educational Society, which is registered under the Societies Registration Act, 1860. St Aloysius College, Mangalore, traces its origins to 1880, when some European Jesuits, who had landed in Mangalore in 1878, started it for the education of youth. In 2005, St. Aloysius College planned to extend its educational enterprises beyond the geographical boundaries of Mangaore in commemoration of its post centenary silver jubilee. As a result, St. Aloysius PU College Harihar was founded. St Aloysius Pre-University College, Harihar, belongs to an international network of educational institutions-schools, colleges, universities-directed by the Society of Jesus, whose members are called Jesuits.

From June 2005, till April 2009, St Aloysius Pre-University College, Harihar was functioning in the space generously provided by the management of Maria Nivas School, Harihar. From May 2009, the college has been functioning in the college premises at Amaravathi.