Social jetlag (SJL) is the difference between the midpoint time of sleep between weekend and weekday. SJL is experienced by many adolescents and is a matter of concern in public health. In private experiences, pupils who were forced to wake up early on non-school day mornings to engage in hard physical activity and who had little time for sleep on non-school nights were identified. These pupils are supposed to show negative SJL values. However, few studies have described pupils with negative SJL values. The current study aimed to raise a hypothesis that pupils with negative SJL might constitute a discrete population with typical characteristic features. A total of 2,722 questionnaires obtained from pupils in grades 5 to 12 were assessed by the multiple comparison test of the Dunnett method to determine significant differences in the lifestyle habits among SJL categories (SJL-I, <0 h; SJL-II, 0–1 h; SJL-III, 1–2 h; SJL-IV, 2 h or more). Pupils with SJL-I were mostly male compared to those in SJL-II. Physical activity score showed a significantly higher value in SJL-I than SJL-II, while that in SJL-III and SJL-IV revealed significantly lower values than that in SJL-II. Contrarily, non-school day screen time and non-school night sleep duration showed significantly lower values in SJL-I than SJL-II, while those in SJL-III and SJL-IV revealed significantly higher values than those in SJL-II. After-school activity score showed a significantly higher value in SJL-I than SJL-II, while that in SJL-III and SJL-IV revealed lower values than that in SJL-II. At least in Japan, a hypothesis that pupils with negative SJL constitutes a discrete population with typical characteristic features (predominantly male, higher physical activity, and after-school activity scores; less non-school day screen time; and shorter non-school night sleep duration) was raised. Further studies are needed to confirm this hypothesis.