In partnership with the District School Board of Niagara, Mutual Support operates three Alternate School classrooms. These classrooms are available to any resident of Mutual Support who requires a higher level of support in the school setting than is typical in the public system. The classrooms are located at Port Colborne High School in Port Colborne, Ontario. Each residence is responsible for transporting the residents to and from school daily. Each classroom is staffed by a DSBN teacher and an MS child care worker. Mutual Support also employs a Supervisor for the school program to support the teachers and staff, develop programming and support the residents. Each resident has an IEP (Individual Education Plan) developed by the classroom teacher. The DSBN teachers are an important member of the Case Management Planning Team for each resident.

Partial integration into public school programs can be facilitated while participating in the Alternate School Program. Students are moved to full integration based on good outcomes and the Plan Of Care process.