St. Michael's High School was founded in 1859 as El Colegio de San Miguel in an adobe hut next to the San Miguel Mission on present-day Old Santa Fe Trail (formerly College Street), in what is now the Barrio De Analco Historic District.

The school was established at the behest of Archbishop Jean-Baptiste Lamy, who had arrived in New Mexico in 1851 to find that formal education in the territory was almost nonexistent.

After establishing the Loretto Academy for girls in 1852, Lamy recruited four De La Salle Christian Brothers from his native France to open a similar school for boys.

Brothers Hilarien, Gondulph, Geramius and Galmier Joseph arrived on October 27, 1859, after two and a half months of travel by ship, train and covered wagon, and St. Michael's held its first classes shortly afterward.

[2] In 1874, the territorial legislature granted the school a charter as the College of the Christian Brothers of New Mexico.

In the early decades of the twentieth century, the St. Michael's science labs were remodeled, a gymnasium, financed by alumni donations, was constructed, and athletic teams began competing in New Mexico's interscholastic sports program.

In 1968 St. Michael's moved to its current location at 100 Siringo Road and became co-educational upon the closing of the Loretto Academy for Girls.

Since 1967 there has been a gradual but steady increase in the number of lay teachers at St. Michael's, as the Brothers grow older and retire.