It was founded by the Grey Nuns in 1869, with the Sisters of the Holy Names of Jesus and Mary assuming responsibility for the school in 1874.

The Academy was located in a rented house on Victoria Street near the centre of population between the intersection of Portage and Main and The Forks, the junction of the Red and Assiniboine Rivers.

In the spring of 1873, when the new province of Manitoba assumed responsibility for education, St. Mary’s began to receive public funding.

Because the arrangement with the Grey Nuns was a temporary one, in 1874 Archbishop Taché recruited the Sisters of the Holy Names of Jesus and Mary, a teaching congregation from Quebec, to work in education in the diocese.

Enrollment at the girls school increased rapidly and the first St. Mary's Academy on Victoria Street was soon filled to capacity.

In 1876 a second small house, called The Annex, was erected, but continued overcrowding necessitated a move to larger quarters on Notre Dame East in 1881, to which a wing was added in 1892.

Once again the facility became inadequate and the Sisters searched for a new location for the third Academy, away from the crowded, noisy, commercial core of the city.

The new Academy, shaped like a “U” was an elaborate structure four stories high with solid brick walls and a mansard roof.

During the 1930s the school survived the ever-increasing taxes on the property, accentuated by the depression, and launched a new period of steady growth in the post-war era.

In June 1960 the boarding school closed, ending a ninety-year-old tradition, and the elementary grades and the College were phased out to help reduce crowding.

The 1964 addition, a large wing including a theatre, library, fine arts studio and gym, was inspired by a desire to enrich the school culturally.

The school is officially opened its new dramatic arts wing complete with props studio, make up/dressing rooms, and costume lab, in September 2013.

It includes the following: St. Mary's Rugby team won the title of City Champion in May 2011, and the Golf, Cross-Country, And Volleyball Provincial Championships for the 2011–2012 Season.

In 1909 a larger building was attached that houses most of the 21 classrooms as well as the Richardson Science Wing, the human ecology department and a computer lab.

Recent renovations and upgrades to meet building code standards and to enhance programs left intact the traditional architecture wherever possible, and also incorporated up-to-date technology, furnishings and equipment, and resulted in a more comfortable learning environment with improved lighting and air-conditioning.

It includes Alumnae Hall, a library, a fine arts studio, the Sister Rita Maureen Gym, a cafeteria and a computer lab.

The gym is home to the St. Mary’s Academy Flames while Alumnae Hall, a 625-seat theatre, houses drama productions, assemblies, school Masses, and meetings.