Milagres Educational Institution was founded by Bishop Rt Rev. Bernardin in 1848 and was entrusted to the care of Mr. John Edward Fitzerald, an Irish man and Monsieur Dupret a Frenchman. In the beginning it was started as a Primary English School with classes added gradually. The Director of Public Instruction Madras, accorded permanent recognition to the School on 23rd July 1929 as an independent Secondary Institution with classes I to V. Sir Merveral Stetham, the then Director of Public Instruction Madras, accorded permission to open High School Classes on 3rd April 1944 and accorded permanent recognition on 5th August 1954.

The government of Karnataka upgraded the High School into a Pre-University with Commerce course on 5th July 1982 and Science section was added in 1999. In the year 2011, girls were admitted, thus making Milagres, a Co-Educational Entity. Milagres Pre-University College, Mangalore is a Christian Religious Minority Institution run by the Catholic Board of Education of the Diocese of Mangalore, is a registered body. Locally it is managed by Milagres Church, Mangalore. It imparts education to all without distinction of caste and creed. Currently we have ten sections comprising of HEBA/EBAC/EBAS in commerce and PCMB/PCMC in Science.