Background We explored whether the maximum predicted walking distance, assessed with six-minute walk test (6MWT) and reflecting submaximal functional exercise capacity, is decreased among patients with pectus excavatum (PEX). Methods This study comprised a retrospective analysis of patients with PEX who underwent a 6MWT for the assessment of functional capacity. The maximum distance walked was recorded and compared to reference values established for different populations, including a young and healthy South American population. Results We included 43 patients with PEX who underwent 6MWT. The mean age was 17.8 ± 6.7 years. The mean maximum distance walked was significantly lower than the predicted distance (600.8 ± 67.6 metres vs. 729.8 ± 67.5 metres, p < 0.0001). Using the Enright reference equation including an older reference population, the mean negative difference was higher (PEX patients walked 190.4 ± 78.4 metres less than predicted, p < 0.0001). We also applied the Li et al. reference equation accounting for sex among other variables, detecting a decreased walked distance compared to the gender-adjusted predicted distance (PEX patients walked a mean 222.4 ± 87.4 metres less than predicted, p < 0.0001). Using the Ulrich et al. equation, PEX patients walked a mean 114.2 ± 85.1 metres less than predicted (p < 0.0001). Although of uncertain clinical relevance, there was a significant decrease in the mean oxygen saturation after exercise (baseline 97.4 ± 1.2%, vs. final 96.4 ± 2.1%, p = 0.006). Conclusions In this study, we identified a significant reduction in the maximum walked distance among patients with PEX compared to the predicted distance, thus potentially emerging as an unsophisticated means to evaluate and quantify functional exercise capacity.