Introduction: emotional exhaustion among trainee teachers is a relevant topic since it could have repercussions regarding the lives of their future pupils. Our objective was to determine the degree of trainee teachers’ emotional exhaustion and associated variables during the COVID-19 pandemic. Methods: the design was cross-sectional and descriptive. Questionnaires with sociodemographic variables, perceptions of mental health, and the Emotional Exhaustion Scale (ECE) (α = 0.890; ω = 0.893) validated for the Chilean context were answered by 204 trainee teachers. The results were analyzed using SPSS software version 25 and the Emotional Exhaustion Interpretation Table (EES-Int). Results: the results show that 92.2% of the trainee teachers presented a worsening in their mental health, stress (66.2%), irritability (38.2%), anxiety (37.7%), and depressive symptoms (32.8%). Online classes (73.04%) and the pandemic (67.6%) were the main influencing factors. Education students who perceived their mental health had worsened became 6.63 times more likely to develop emotional exhaustion [AOR = 6.63; 95% CI: 1.78, 24.69]. In addition, education students with a high perception of academic stress were 7.45 more likely to develop emotional exhaustion [AOR = 7.45; 95% CI: 1.98, 28.09]. Conclusion: we can conclude that trainee teachers have high levels of emotional exhaustion and their perception of their mental health and the academic stress they are being subjected to during the COVID-19 pandemic may lead them to present symptoms of frequent or permanent problems with concentration, attention, recall of information, dissatisfaction with their performance, and frequent learning difficulties. From the affective dimension, they present frequent or permanent anxiety, restlessness, irritability, indifference, low mood, and psychomatization. From the socio-interactional dimension, they present frequent or permanent social withdrawal, interpersonal problems, problems at work or school, and family and relationship problems. Increasing the sample to delve into emotional exhaustion by subject area is necessary. For future studies, research should be conducted on the causes of emotional exhaustion by subject area and the coping strategies of trainee teachers to understand differences and provide input on emotional support in practice.