Understanding factors associated with physical activity (PA) is important to promote PA. The purpose of the present study was to investigate factors associated with achieving PA guideline in 293 Japanese adolescents (140 boys and 153 girls). Time spent in moderate to vigorous PA (MVPA) was accessed by using accelerometers. Based on MVPA, the participants were classified as “Active” (≥60 min/day of MVPA) or “Inactive” (<60 min/day of MVPA). Anthropometry, age, screen time, mental health, participation in after-school sport activities, sleep status, and breakfast status were measured as factors potentially associated with achieving PA guideline. Adjusted logistic regression analyses revealed that after-school sports activities were positively associated with the probability of being Active for both sexes (odds ratios [ORs] [95% confidence intervals (CI)] = 3.90 [1.13-13.49] for boys, 4.80 [1.80-12.81] for girls). In addition, body fat was negatively associated with a reduced likelihood of being Active for girls (ORs [95%CI] = 0.93 [0.87-0.97]). Two factor ANOVA revealed that those in Inactive group had significantly lower PA levels than those in Active group on both regular curriculum and extra-curriculum (F _{(1, 138)} = 152.50 for boys, F _{(1, 151)} = 181.95 for girls, p < 0.001). In addition, for girls, there was a significant interaction effect between domain (regular curriculum vs. extra-curriculum) and after-school sport activities (F _{(1, 151)} = 4.91, p = 0.028), suggesting that obtaining higher PA levels on extra-curriculum might be difficult for those who do not belong to any after-school sport activities. Therefore, promoting PA on regular curriculum (i.e., physical education lessons and recess) might be alternative ways to increase PA levels for those individuals. Furthermore, special attention may be needed for girls who have higher body fat to promote PA.