Academic burnout has serious negative consequences for both physical and mental health of college students. Therefore, studies trying to find the protective factors are beginning to emerge. The main research question was to assess whether flow experienced in different domains of students' life can be a protective factor of their academic burnout. Since longitudinal studies that would determine whether flow experienced in different activities prevents academic burnout are lacking, the aim of this study was to assess whether flow in academic and leisure activities predict longitudinal changes in students' academic burnout and to what extent. Using a two-wave cross-lagged panel design, the current study examined academic flow, flow in leisure activities and academic burnout in 160 first year students of University of Zagreb. Burnout and flow were assessed in two time waves: one month after beginning of the academic year, and then after 8 months, at the end of the academic year. Structural equation modeling was employed to test a series of competing models. Direct model with a path from flow in academic activities and leisure at the beginning of the academic year to burnout at the end of the academic year provided acceptable model fit. Academic flow was related to less, and flow in leisure activities to more subsequent academic burnout. The study suggests that enhancing flow experiences in academic activities may be relevant for reducing students' burnout. At the same time, results suggest that many leisure activities, although flow inducing, may be counterproductive for preventing students' burnout.