Elizabeth Seton Academy began with the announcement in January of 2003 that Msgr. Ryan Memorial High School (MRM) in Dorchester, MA, would close. This news was received with great sadness by its faculty, staff, parents, students, and the Sisters of Charity, Halifax, who began the school in 1918. MRM (previously known as St. Margaret High School) had provided excellent and affordable single-gender Catholic education for the young women of the Dorchester, South Boston, and Roxbury areas of Boston for 85 years.

Following the announcement, a concerned group of MRM alumnae, friends, and Sisters of Charity studied the feasibility of opening a new school to continue the mission of MRM. In two short months, after intense research, planning, and prayer, on March 25, 2003, Elizabeth Seton Academy became a legally incorporated entity in the Commonwealth of Massachusetts and a Board of Directors was established. Approval to operate as a Catholic school in the Archdiocese of Boston was granted on July 18, 2003, and a mere six weeks later, on Sept. 8, 2003, Elizabeth Seton Academy opened its doors to its first classes at the site of the former St. Gregory Parish High School in Dorchester.

The school's mission was to educate young women by developing their potential as scholars, instilling in them a sense of social responsibility and empowering them to become the leaders and professionals of tomorrow. The young women were challenged to develop their unique abilities through a strong sense of self in a community that embraced religious, cultural, and ethnic diversity. The image and motto that inspired its planners was that of St. Elizabeth Ann Seton, Hazard yet Forward. Motivated by Elizabeth's courageous spirit and passion for education, Elizabeth Seton Academy was committed to move forward as it embraced the challenges of its mission.

There was a cohort of Sisters of Charity who worked and/or volunteered at Elizabeth Seton Academy over the years. Founding members included Sisters Anne Fahey, Sally McLaughlin, Esther Plefka, Maryanne Ruzzo, and Sister Joanne Westwater, RGS. Sisters were also among the faculty: Sisters Mary Anne Foster, Elaine Nolan, Martha Westwater, and Grace McColgan.

After 13 successful years, the challenges for Elizabeth Seton Academy to continue had become insurmountable and the school closed in 2016. The remaining students continued on their paths to success at several other Catholic Schools, which warmly welcomed them for the duration of their high school years.