The aim of this study was to assess the impact of the COVID-19 pandemic on the mental wellbeing of children 8–18 years old with chronic conditions, by comparing pandemic data with pre-pandemic data and with healthy peers. Data were obtained from two ongoing longitudinal cohorts: the PROactive cohort study following children with a chronic condition, and the WHISTLER population cohort. Mental wellbeing was assessed by three indicators: life satisfaction, internalising symptoms, and psychosomatic health. The stringency of the COVID-19-related lockdown was considered a moderating factor. Data on chronic patients were recorded before (n = 934, 65% girls) and during (n = 503, 61% girls) the pandemic, and compared to healthy peers during the pandemic (n = 166, 61% girls). Children with a chronic condition reported lower life satisfaction, but no clinically relevant changes in internalising symptoms or psychosomatic health, during the pandemic compared to before. In comparison to healthy peers, children with a chronic condition experienced decreased life satisfaction and psychosomatic health, but internalising symptoms did not differ between groups during the COVID-19 pandemic. The lockdown stringency was negatively associated with all indicators of mental wellbeing—worse life satisfaction, more internalising symptoms, and more psychosomatic symptoms.