Introduction How cardiorespiratory function changes following the surgical correction of pectus excavatum (PE) often gives mixed results, with meta-analyses demonstrating no benefit in terms of pulmonary function but improvement in cardiac function. Functional responses may depend on type of surgery, follow-up time and/or the patient’s presurgical functional status, and debate persists on the purely aesthetic nature of such surgery. The aim of this protocol is to analyse data describing lung function and incremental exercise testing before vs after the surgical correction of PE.Methods and analysis A historical-prospective before–after surgical correction of PE cohort will be constituted. Historical inclusions are recruited during follow-up visits at approximately 12, 24, 36 or 48 months following a prior surgery (with presurgical data mined from patient records). Prospective inclusions are recruited during presurgical work-ups and followed for 1 year following surgery. The data collected include spirometry, incremental exercise testing, body mass index, body composition, questionnaires targeting general health status, self-esteem and body image. Any complications due to surgery are also described.The primary outcome is oxygen pulse during incremental exercise testing, and 44 data points are required to demonstrate a moderate postsurgical change (ie, a Cohen’s effect of d=0.5). Wilcoxon signed-rank tests or t-tests for paired data will be used for before–after comparisons (with false discovery rate corrections for secondary analyses).Ethics and dissemination This study will be conducted according to the principles of the Declaration of Helsinki (as revised in 2013) and was approved by a randomly assigned, independent, ethics committee (Comité de Protection des Personnes Sud-Méditerranée II, reference number: 218 B21) as per French law on 6 July 2018. Informed, written consent for study participation is required of all study candidates prior to enrolment. Results will be published in an international peer-reviewed journal.Trial registration number NCT03770390; Clinicaltrials.gov