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Background Descriptions of the COVID-19 pandemic’s indirect consequences on children are emerging. We aimed to describe the impacts of the pandemic on children with medical complexity (CMC) and their families. Methods A one-time survey of Canadian paediatricians using the Canadian Paediatric Surveillance Program (CPSP) was conducted in Spring 2021. Results A total of 784 paediatricians responded to the survey, with 70% (n = 540) providing care to CMC. Sixty-seven (12.4%) reported an adverse health outcome due to a COVID-19 pandemic-related disruption in healthcare delivery. Disruption of the supply of medication and equipment was reported by 11.9% of respondents (n = 64). Respondents reported an interruption in family caregiving (47.5%, n = 252) and homecare delivery (40.8%, n = 218). Almost 47% of respondents (n = 253) observed a benefit to CMC due to COVID-19 related changes in healthcare delivery, including increased availability of virtual care and reduction in respiratory illness. Some (14.4%) reported that CMC were excluded from in-person learning when their peers without medical complexity were not. Conclusion Canadian paediatricians reported that CMC experienced adverse health outcomes during the COVID-19 pandemic, including disruptions to family caregiving and community supports. They also describe benefits related to the pandemic including the expansion of virtual care. These results highlight the need for healthcare, community and education policymakers to collaborate with families to optimize their health.