People living with rare diseases had a high risk of negative health outcomes due to COVID-19. Pandemic preparedness will ensure best practice procedures and optimal outcomes during future pandemic events. This paper sought to understand the needs of children with rare diseases during the COVID-19 pandemic to inform preparation for future pandemic and disaster events. First, impacts and outcomes from the COVID-19 pandemic on people living with rare disease were identified in the literature. The literature demonstrated that the COVID-19 pandemic had significant and multiple impacts on people with rare diseases. Second, a qualitative descriptive study was conducted, involving members of 17 families with a child with a rare neuromuscular disorder in 2021, to explore COVID-19 pandemic experiences. Qualitative data coded to Bronfenbrenner’s socio-ecological systems model and described impacts on the child’s physical (e.g., respiratory infections), mental (e.g., anxiety), and social (e.g., maintaining connections) health and wellbeing. Families reported resilience and risk factors in their interactions with health and therapy services, and education. Families valued diseases specific information and heightened awareness of infection control across the community. Third, public health guidelines for emergency preparedness were examined to inform recommendations for pandemic and disaster preparedness for people living with rare diseases. Guided by the literature, qualitative data and disaster management frameworks, recommendations that aim to prevent diagnostic delay, optimise coordination of health and social supports, improve education, planning and training, and maintain research and development were identified. The importance of pandemic preparedness for children with rare diseases cannot be understated. Risk and resilience factors in the context of highly individual requirements inform lessons for children living with rare diseases. This study informs future policy and procedure preparation for future pandemic events and other disasters to optimise healthcare of children with rare diseases.