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Motivation and emotion in learning is a burgeoning field of research. However, the relationship between the two remains inconclusive. This paper aims to examine gender-specific relationships among achievement goal orientations and achievement emotions in 24 medical students during clinical diagnosis in a computer-based learning environment. Correlation and regression analysis were conducted. As expected, mastery-approach goals correlate with positive emotional outcomes. Mastery-avoidance correlates with and predicts undesirable emotional outcomes regardless of gender. Our findings reveal some gender-specific relationships between AGOs and AEs: (a) performance-avoidance negatively correlates with females’ hope; (b) mastery-avoidance positively correlates with males’ shame. Performance-oriented goals did not predict emotions in this study. Our results could inform medical schools to cultivate adaptive AGOs and emotions that address gender profiles.