Purpose: We aimed to evaluate the levels of Burnout Syndrome (BS) in Agricultural Sciences students, both before and during the COVID-19 pandemic period. Design/methodology/approach: We accessed 77 students for Burnout Syndrome using the Maslach Burnout Inventory-Student Survey (MBI-SS) on two occasions, the first in February and the second in October 2020. Sixty-three students completed both phases. The data were analyzed in a mixed factorial scheme (Three-way ANOVA; p < 0.05). Findings: Academic efficacy improved over time without interference of sex or physical activity frequency (p < 0.001). The emotional exhaustion domain significantly reduced over time in women who declared to practice physical activity (p = 0.037). A similar effect was observed in both men and women for the cynicism domain (p < 0.001). Online teaching strategies and the regular practice of exercise were associated to reduced levels of BS during the pandemic. Practical implications: The adoption of the emergency remote education system (ERE) associated with the practice of exercise can mitigate the harmful effects of the COVID-19 quarantine on the mental health of students. Theoretical implications: The ERE can be an effective strategy to mitigate BS levels in Agricultural Science students in the post-pandemic period. Originality/Value: This is the first study that presents results of BS in students of Agricultural Sciences, comparing before and during the COVID-19 pandemic.