Living with a long-term medical condition is associated with heightened risk for mental health and psychosocial difficulties, but further research is required on this risk for children and adolescents with a rare disease in the educational setting. The aim of this study is to describe parents’ perceptions of the psychosocial impact of rare diseases on their school-aged children in Western Australia. A cross-sectional survey of 41 parents of school-aged children and adolescents diagnosed with a rare disease completed an online questionnaire. Questions related to their perceptions of health-related stigma, bullying, social competencies and mental health difficulties faced by their child. Results showed that stigmatisation was experienced by 75.6% of participants, and almost half (46.4%) reported their child was bullied. In this sample, parents reported high sensory (vision and hearing) abilities, but low to moderate self-care competence in relation to social activities and peer relations. Almost half of the respondents (43.9%) reported mental health difficulties among their children. Children and adolescents with a rare disease have unique psychological and social issues. These findings highlight the need for greater efforts to meet the diverse psychosocial, physical and emotional needs of children diagnosed with a rare disease who attend mainstream schools in Western Australia.