Introduction Epidural analgesia is currently considered the gold standard in postoperative pain management for the minimally invasive Nuss procedure for pectus excavatum. Alternative analgesic strategies (eg, patient-controlled analgesia and paravertebral nerve block) fail in accomplishing adequate prolonged pain management. Furthermore, the continuous use of opioids, often prescribed in addition to all pain management strategies, comes with side effects. Intercostal nerve cryoablation seems a promising novel technique. Hence, the primary objective of this study is to determine the impact of intercostal nerve cryoablation on postoperative length of hospital stay compared with standard pain management of young pectus excavatum patients treated with the minimally invasive Nuss procedure.Methods and analysis This study protocol is designed for a single centre, prospective, unblinded, randomised clinical trial. Intercostal nerve cryoablation will be compared with thoracic epidural analgesia in 50 young pectus excavatum patients (ie, 12–24 years of age) treated with the minimally invasive Nuss procedure. Block randomisation, including stratification based on age (12–16 years and 17–24 years) and sex, with an allocation ratio of 1:1 will be performed.Postoperative length of hospital stay will be recorded as the primary outcome. Secondary outcomes include (1) pain intensity, (2) operative time, (3) opioid usage, (4) complications, including neuropathic pain, (5) creatine kinase activity, (6) intensive care unit admissions, (7) readmissions, (8) postoperative mobility, (9) health-related quality of life, (10) days to return to work/school, (11) number of postoperative outpatient visits and (12) hospital costs.Ethics and dissemination This protocol has been approved by the local Medical Ethics Review Committee, METC Zuyderland and Zuyd University of Applied Sciences. Participation in this study will be voluntary and informed consent will be obtained. Regardless of the outcome, the results will be disseminated through a peer-reviewed international medical journal.Trial registration number NCT05731973.