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While a wide range of studies report specific individual attributes and burnout are associated with work-based learning and performance outcomes, little empirical investigations elucidate the factor relationship. Effective instructional planning requires understanding the developmental trajectories of the learner to targeted expectancy outcomes. Thus, the purpose of this study is to examine the moderating effect of workplace burnout among surgical residents on the relationship between their attributes of learner autonomy and their learning outcomes in a hospital-based competency training program. In a prospective longitudinal cohort design, the study data confirmed the positive relationship between learner autonomy and achievement measures. Further, it revealed the moderation effect of burnout on the relationship change. Burnout is a significant risk in their learning experience.