Saint Mary School offers advanced courses in Middle School, based upon performance scores and teacher recommendations. In Grades 6, 7 and 8, Advanced Math and Advance ELA are offered.

The Advanced Math program prepares students for the Grade 9 Regents Algebra I course that is offered in Grade 8.

Advanced ELA provides more in-depth work in literature and writing for accelerated students and prepares them for Honors ELA programs in high school.

The Regents Living Environment course is also available to qualifying students in Grade 8 science.