In 1989 the school began a junior high school starting with a 7th grade class only, with an 8th grade class added the following year.

St. Mary's incorporated in 2006 as a private school, independent from the Archdiocese of Boston, and instituted a new governance structure with a head of school, principal, and twenty-member Board of Trustees, thus ending its period as a parochial school.

The result: 100 consecutive games without a loss over three years before a loss to Hingham in the state semi-finals, and three Massachusetts Division 1 State Titles.

[3] The former Girls High School building was demolished in 2005 to make way for the state-of-the-art William F. Connell Center, which provides a library, technology center, chapel, and classrooms.

Students are encouraged to participate in Christian service activities, such as Rachel's Challenge, Sant' Edigio, and assisting at My Brother's Table, a local food pantry.