Objective To report the prevalence of lower airway dysfunction in athletes and highlight risk factors and susceptible groups. Design Systematic review and meta-analysis. Data sources PubMed, EBSCOhost and Web of Science (1 January 1990 to 31 July 2020). Eligibility criteria Original full-text studies, including male or female athletes/physically active individuals/military personnel (aged 15–65 years) who had a prior asthma diagnosis and/or underwent screening for lower airway dysfunction via self-report (ie, patient recall or questionnaires) or objective testing (ie, direct or indirect bronchial provocation challenge). Results In total, 1284 studies were identified. Of these, 64 studies (n=37 643 athletes) from over 21 countries (81.3% European and North America) were included. The prevalence of lower airway dysfunction was 21.8% (95% CI 18.8% to 25.0%) and has remained stable over the past 30 years. The highest prevalence was observed in elite endurance athletes at 25.1% (95% CI 20.0% to 30.5%) (Q=293, I 2 =91%), those participating in aquatic (39.9%) (95% CI 23.4% to 57.1%) and winter-based sports (29.5%) (95% CI 22.5% to 36.8%). In studies that employed objective testing, the highest prevalence was observed in studies using direct bronchial provocation (32.8%) (95% CI 19.3% to 47.2%). A high degree of heterogeneity was observed between studies (I 2 =98%). Conclusion Lower airway dysfunction affects approximately one in five athletes, with the highest prevalence observed in those participating in elite endurance, aquatic and winter-based sporting disciplines. Further longitudinal, multicentre studies addressing causality (ie, training status/dose–response relationship) and evaluating preventative strategies to mitigate against the development of lower airway dysfunction remain an important priority for future research.