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Background Fever in children with SARS-CoV-2 infection may increase the risk of intraoperative oxygen desaturation during surgery. This study seeks to find the optimal surgery timing by examining oxygen desaturation rates after fever resolution.Methods A prospective cohort study from March to August 2023 included children with SARS-CoV-2 infection who were scheduled for surgery after fever resolution. The primary outcome was the incidence of intraoperative oxygen desaturation. Logistic regression models were used to calculate the adjusted incidence of oxygen desaturation, stratified by time intervals from fever resolution to the day of surgery: 0–2 weeks, 3–4 weeks, 5–6 weeks, 7–8 weeks and ≥3 months.Results The intraoperative oxygen desaturation rate was 7.96%. It was highest in the 0–2 weeks group (18.3%), lower in the 3–4 weeks group (11.5%), and further decreased in the 5–6 weeks (6.8%), 7–8 weeks (4.7%) and ≥3 months (4.9%) groups. Adjusted analysis showed significantly higher oxygen desaturation risk in the 0–2 weeks (adjusted OR (aOR), 5.56; 95% CI 3.76 to 8.21) and 3–4 weeks (aOR, 3.31; 95% CI 2.15 to 5.09) groups compared with the ≥3 months group. Risk factors for intraoperative oxygen desaturation included younger age, higher Body Mass Index (BMI), an abnormal chest radiograph and ongoing symptoms (all p<0.05).Conclusions To minimise the risk of intraoperative oxygen desaturation, elective surgeries in paediatric patients should be scheduled no earlier than 4 weeks after fever resolution.Trial registration number The study was registered at Chinese Clinical Trial Registry http//www.chictr.org.cn/ (Registration date 13/03/23 Trial ID ChiCTR2300069293).