All schools are encouraged to participate in the survey, however participation is not mandatory. This includes public, nonpublic, charter and tribal schools, as well as alternative learning centers and juvenile correctional facilities. No financial incentives are offered to districts, schools or students. Students in grades 5, 8, 9, and 11 are eligible to take the survey, and schools may choose to include additional grades (6, 7, 10, and 12) if they wish. In 2022, over 135,000 Minnesota students in grades 5, 8, 9, and 11 participated in the survey.

At the beginning of the school year, the Minnesota Department of Education (MDE) sends emails to superintendents, principals and District Assessment Coordinators (DACs) with details about the survey and instructions for registering their schools for that year's administration of the MSS. DACs are directed to an online registration system where they can indicate the grades they wish to survey and the planned administration date for each school in their district. After registering, DACs receive instructions for administering the survey to distribute these instructions to schools. Additionally, MDE staff, local public health representatives and others who rely on MSS data follow up with non-registered schools to encourage their participation. Schools have until one week before the end of the fielding period to complete their registration.