The aim of this pilot study was to characterize seasonal variation in the moderate to vigorous physical activity (MVPA) and sedentary behavior of Portuguese school youth, and understand the influence of activity choices and settings. The participants in this study were 24 students, aged 10-13 years. Accelerometers measured daily PA over 7 consecutive days, in different seasons May - June and January - February. In summer, boys accumulated more minutes in MVPA (928 minutes/week) than girls (793 minutes/week). In winter the pattern was reversed with girls accumulating more activity than boys (736 minutes/week vs. 598 minutes/week). The repeated measures ANOVA revealed significant effects for season (F = 5.98, p = 0.023) and in- school vs. out-of-school (F = 6.53, p = 0.018). Youth were more active in the summer and activity levels were higher after school than in school. Summer season provided relevant contexts for youth physical activity accumulation. Winter season may have been a significant barrier to boy’s preferred PA context. Differences in choices of outdoor or indoor PA, after school, explained the gender differences in seasonal activity patterns.