Academic burnout has become a growing concern in health sciences education, where high academic and emotional demands place students at particular risk of emotional exhaustion. Drawing on Social Cognitive Theory and the Control-Value Theory of Achievement Emotions, this cross-sectional, descriptive–correlational study examined the roles of motivational resources (self-efficacy and self-determination) and achievement emotions (boredom) in predicting emotional exhaustion among 442 undergraduate students from a public university in Northern Chile. Participants completed validated scales assessing all four constructs, and data were analyzed using confirmatory factor analysis and hierarchical linear regression. Descriptive results indicated moderate to high levels of self-efficacy and self-determination, moderate levels of emotional exhaustion, and moderate to low levels of boredom. Bivariate analyses revealed that self-efficacy and self-determination were positively correlated (r = .517, p < .001), and both showed negative correlations with boredom (r = −.245 and r = −.180, respectively; p < .001). Emotional exhaustion was positively and moderately correlated with boredom (r = .392, p < .001) and negatively correlated with self-efficacy (r = −.192, p < .001), whereas its correlation with self-determination was not statistically significant (r = .032, p > .05). Hierarchical regression identified boredom as the strongest predictor of emotional exhaustion (β = .379, p < .001), with the full model explaining 19.5% of its variance (R² = .195, adjusted R² = .189). Self-efficacy emerged as a significant protective factor (β = −.206, p < .001), whereas self-determination showed a suppressive effect in the full model. These findings highlight the central role of boredom as an emotional pathway to exhaustion in health sciences students and underscore self-efficacy as a key protective resource, with implications for early psychoeducational interventions in regional university contexts.