Student Council is an organization conducted by student leaders and supervised by adult sponsors. The purpose of Student Council is to provide leadership, and to serve the student body, the school, and the community. Student Council at Stonybrook Intermediate and Middle School is the students' voice in our school.

Student Council is open to students in 7th and 8th grade at Stonybrook. In order to represent the appropriate grade-level as a Student Council Representative a completed application must be turned in by the stated due date. Candidates must obtain signatures from students and recommendations from teachers. In addition, students can have no grade lower than a C and they must maintain an A in citizenship.

Stonybrook's Student Council meets after the regular school day.

Most of the projects completed by Stonybrook's Student Council are service-oriented. Student Council coordinates activities such as canned food drives, book drives, clothing drives, fundraisers for various organizations, spirit weeks, grade level competitions, essay and poster contests, and other activities as they arise for the student body and staff.