Background: Adolescents with intellectual and developmental disability (IDD) are reported to have lower uptake of routine vaccines than their peers. Little research has explored stakeholders' perceptions and support of school-based vaccinations for this population in NSW, Australia. Methods: Focus groups and interviews were conducted with four stakeholder groups involved in the vaccination program in special education schools in New South Wales, Australia: students with IDD, parents, education staff, and health professionals. Results: Stakeholders mostly supported vaccinating adolescents with IDD in school settings. Students valued the familiar environment and emotional support from teachers. Parents appreciated the convenience and accessibility of the program. Education staff regarded vaccinations as vital for student health and mostly supported school-based delivery but faced practical and ethical challenges, such as insufficient resourcing, confusion around holding students for safety and emotional support, and concerns about losing students' trust in the school as a safe environment if vaccination was experienced as traumatic. Health staff identified a need for better prevaccination communication with families and schools to improve vaccine uptake and student preparation. Conclusion: Findings highlight a need for increased support for special schools that act as key program facilitators between those who deliver and those who receive this vital health service.