This study aimed to determine the relationship between affective structures and academic burnout among male and female third-grade high school students in Zahedan in the academic year 2016-2017. The current descriptive-correlational study had a sample including 362 students selected using a multistage cluster sampling method. To collect data, Academic Burnout Questionnaire (Berso et al., 1997) and Positive and Negative Affect Schedule (Watson et al., 1988) were used. Results of the present study indicated that positive affect was significantly and diversely correlated to subscales of academic burnout (academic fatigue, academic apathy, and academic inefficiency). Moreover, negative affect was significantly and directly correlated to all the subscales of academic burnout. Results of an independent t-test demonstrated that there were no significant differences between the male and female students with regard to positive and negative eafects. However, academic burnout was higher among the male students compared to their female counterparts. Furthermore, results of a stepwise regression analysis showed that in the first step, positive affect alone predicted 22% of the variance in academic burnout and, in the second step, negative affect increased the power of predicting academic burnout to 28%. Given the predictive power of affective structures (28.2%, p<0.001), they can be affectively applied to prevent academic burnout.