Archbishop Thomas Edmund Molloy had a hand in the birth of TMLA due to his conviction that the girls of the Diocese of Brooklyn deserved an academy of their own.

While traveling on the Long Island Rail Road in early 1932, Mother Mary Louis, the General Superior of the Sisters of St. Joseph, selected the hilltop, the Fox/Adikes estate "Rose Crest," in the countryside of Jamaica Estates as her site for an academy;[4] however, Mother Mary Louis died on May 22, 1932.

[5] Later, the hilltop was purchased by the Passionist priests of the neighboring Immaculate Conception Monastery with the intent to build a high school seminary for boys at that location.

Archbishop Thomas Molloy intervened and convinced the Passionists to sell the estate to the Josephites for exactly the same price they had paid for it themselves.

The architect of the academy's building, Henry Murphy, stated that he wanted to evoke the feel of the private prep schools found in New England.

James Nelson, the builder of TMLA, celebrated the birth of his daughter during the building's construction by naming her for the Academy.

The first students were fifteen young women who were greeted by a faculty of eight sisters for the first day of school on September 14, 1936.

In 1938, TMLA also opened the doors to The Mary Louis Kindergarten, a one-year preschool program for 5-year-old girls and boys.

The original cafeteria, DeChantal Hall, was redesigned into a seven-room music complex; the original locker room became the ten-room guidance complex; the reception parlor became the general office; and a laboratory, a cafeteria, a locker room, and several classrooms were introduced.

In the early 2000s, the auditorium was retooled with restored lighting, a refurbished stage, updated flooring, cushioned seats, and air conditioning.

This expansion and renovation added over 12,500 square feet to the academy's facilities, including a student lounge, art solarium, robotics/engineering laboratory, mathematics laboratory, culinary arts center, an 11-bedroom overnight student retreat facility, and a return to the original mission-style chapel.

[8] The Mary Louis Academy TMLA sponsors athletic teams in 13 separate areas of interest, including Badminton, Basketball, Bowling, Cheerleading, Dance, Golf, Lacrosse, Soccer, Softball, Swimming, Tennis, Track, and Volleyball.