Academic burnout is a serious problem associated with long-term adaptation and falling off the educational track. The current study aimed to examine burnout at two time-points and its associations with cognitive emotion regulation strategies (CERS) frequently used by adolescents ("refocus on planning," "positive refocusing," "rumination") among 326 Estonian middle school students (165 girls). Multigroup SEM of burnout and CERS overall revealed no significant gender differences; "rumination" yielded most robust associations with burnout for both genders cross-sectionally but only for girls longitudinally. Girls also reported significantly higher levels of burnout, and the overall model showed considerably better explanatory power for girls. In addition to discussing specific gender-differences between CERS and burnout, a case is made to (re)introduce depersonalisation to the assessment of burnout in the school context. Results highlight the practical value of addressing the use of maladaptive CERS and encourage future work on (re)conceptualising specific burnout dimensions in various groups.