Introduction The association between viral infections and pulmonary exacerbations in children with cystic fibrosis (cwCF) is well established. However, the question of whether cwCF are at a higher risk of COVID‐19 or its adverse consequences remains controversial. Methods We conducted an observational, multicenter, cross‐sectional study of cwCF infected by severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) between March 2020 and June 2022, (first to sixth COVID‐19 pandemic waves) in Spain. The study aimed to describe patients' basal characteristics, SARS‐CoV‐2 clinical manifestations and outcomes, and whether there were differences across the pandemic waves. Results During study time, 351 SARS‐CoV2 infections were reported among 341 cwCF. Median age was 8.5 years (range 0–17) and 51% were female. Cases were unevenly distributed across the pandemic, with most cases (82%) clustered between November 2021 and June 2022 (sixth wave, also known as Omicron Wave due to the higher prevalence of this strain in that period in Spain). Most cwCF were asymptomatic (24.8%) or presented with mild Covid‐19 symptoms (72.9%). Among symptomatic, most prevalent symptoms were fever (62%) and increased cough (53%). Infection occurring along the sixth wave was the only independent risk factor for being symptomatic. Just eight cwCF needed hospital admission. No multisystem inflammatory syndrome, persisting symptoms, long‐term sequelae, or deaths were reported. Conclusions Spanish current data indicate that cwCF do not experience higher risks of SARS‐CoV‐2 infection nor worse health outcomes or sequelae. Changes in patients' basal characteristics, clinical courses, and outcomes were detected across waves. While the pandemic continues, a worldwide monitoring of COVID‐19 in pediatric CF patients is needed.