In this study, a quantitative diary design was used to examine within-person relationships among daily negative events, emotional intelligence facets, and levels of academic exhaustion and engagement. The research was conducted with a sample of 63 Portuguese health science students (48 females and Mage = 22.3 years) from medicine (n = 33) and psychology (n = 30) degrees who completed a daily survey for 2 weeks (550 diary entries). The results showed a positive association between daily negative events and exhaustion, whereas daily negative events were not associated with academic engagement. Furthermore, the use of emotions emerged as a key emotional intelligence facet associated with reduced exhaustion and enhanced engagement over and above negative events. Taken together, these data highlight the use of emotions as a salient emotional intelligence facet in the context of daily academic exhaustion and engagement. Although preliminary, these findings have the potential to inform emotional intelligence facets that could be improved through training intervention as a means to enhance positive functioning within the higher education environment.