AimTo investigate the evolution of clinical symptoms of COVID‐19 in children throughout the pandemic.MethodsIn this national prospective surveillance study, symptoms in children hospitalised with COVID‐19 were collected from all paediatric hospitals in Switzerland between March 2020 and March 2023. Data was analysed across four time periods, according to the predominantly circulating SARS‐CoV‐2 variant: T1 (wild‐type), T2 (Alpha), T3 (Delta) and T4 (Omicron), as well as by age group.ResultsThe study included 1323 children. The proportion of children admitted to an intensive care unit remained stable throughout the pandemic. However, the pattern and frequency of clinical manifestations changed over time. Respiratory symptoms were less prevalent during T1 (wild‐type), fever during T2 (Alpha) and rash during T4 (Omicron). In contrast, fever and neurological symptoms were more prevalent during T4 (Omicron). Newly described symptoms during T4 (Omicron) included conjunctivitis, laryngotracheitis and seizures. Fever was more prevalent among neonates and infants whereas respiratory symptoms were more common among infants. Gastrointestinal symptoms were more frequent among toddlers, while both toddlers and school‐aged children presented with neurological symptoms more often than other age groups.ConclusionContinuous surveillance is required to detect changes in manifestations and there by be prepared for the optimal management of complications in children with COVID‐19.