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Introduction Previous studies have indicated that exposure to anaesthetics has potential neurotoxic effects, particularly in cases of multiple and long-term general anaesthesia. However, there is currently no research exploring the relationship between early anaesthesia and neurological development in children with congenital scoliosis, who may require multiple surgical treatments. Herein, we present our design for a prospective longitudinal observational cohort study, assessing the long-term impact of general anaesthesia for surgery before school age on neurocognitive function and behaviour in children with congenital scoliosis.Methods and analysis A dynamic cohort of children aged 6–16 years diagnosed with congenital scoliosis between July 2020 and December 2025 in the Department of Orthopaedic Surgery at a tertiary hospital will be enrolled, with an aim to include 150 patients. Detailed information about baseline characteristics, previous anaesthesia and surgery will be collected from medical records, parents or guardians. Neurodevelopment will be evaluated using the abbreviated version of the Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) for neurocognition, and parent-report Achenbach Child Behaviour Checklist and Strengths and Difficulties Questionnaire for neurobehaviour. Repeated measures will be performed during follow-up, with at least a 1-year interval from the previous assessment, whenever the participants are available. The primary outcome is the full-scale intelligence quotient estimated by the WISC-IV. A linear mixed effects model will be constructed, with exposure group —categorised as none, single or multiple anaesthesia exposures based on all episodes of general anaesthesia for surgery before the age of 7 years—as a fixed effect and subject-specific random effects intercept.Ethics and dissemination The study was approved by the Institutional Review Board of Peking Union Medical College Hospital (S-K1093). Written informed consents will be obtained from the parents or guardians. The results of this research will be disseminated through peer-reviewed publications and conference presentations, and shared with paediatric surgical patients and their families who are concerned about the potential neurotoxicity of anaesthesia in clinical practice.Trial registration number NCT06315933.