Scholastic factors (academic achievement) are hypothesized to be important determinants of health-related behaviors in adolescents, but there is a lack of knowledge on their influence on physical activity levels (PAL), especially considering the COVID-19 pandemic and the imposed lockdown. This study aimed to investigate the associations between scholastic factors and PAL before and during the pandemic lockdown. The participants were adolescents form Bosnia and Herzegovina (n = 525, 46% females), who were observed prospectively at the baseline (before the pandemic lockdown) and during the lockdown in 2020 (follow-up). The scholastic factors (grade point average, behavioral grade, school absences, unexcused absences) were evidenced at the baseline (predictors). The outcome (PAL) was evaluated using the Physical Activity Questionnaire for Adolescents at the baseline and the follow-up. Gender, age, parental/familial conflict, and sport participation were observed as confounders. No significant influence of the predictors on PAL were evidenced at the baseline or at the follow-up. The scholastic variables were significantly associated with the changes of PAL which occurred due to pandemic lockdown, with a lower risk for negative changes in PAL among adolescents who were better in school (OR = 0.56, 95%CI: 0.34–0.81, and OR = 0.66, 95%CI: 0.34–0.97, for the grade point average and behavioral grade, respectively). Students who do well in school are probably more aware of the health benefits of proper PAL, and therefore are devoted to the maintenance of their PAL even during the home-confinement of lockdown. Public health authorities should focus more on helping adolescents to understand the importance and benefits of proper PAL throughout the school system.