The uptake of human papilloma virus (HPV) and other adolescent vaccinations in special schools for young people with disability is significantly lower than in mainstream settings. This study explored the factors believed to influence parental decision making regarding vaccine uptake for students with intellectual disability and/or on the autism spectrum attending special schools in New South Wales, Australia, from the perspective of all stakeholders involved in the program. Focus groups and interviews were conducted with 40 participants, including parents, school staff, and immunisation providers. The thematic analysis identified two themes: (1) appreciating diverse parental attitudes towards vaccination and (2) educating parents and managing vaccination questions and concerns. While most parents were described as pro-vaccination, others were anti-vaccination or vaccination-hesitant, articulating a marked protectiveness regarding their child's health. Reasons for vaccine hesitancy included beliefs that vaccines cause autism, concerns that the vaccination may be traumatic for the child, vaccination fatigue following COVID-19, and assumptions that children with disability will not be sexually active. Special school staff regarded the vaccination information pack as inadequate for families, and nurses described limited educational impact resulting from minimal direct communication with parents. More effective communication strategies are needed to address vaccine hesitancy among parents with children with disability.