Purpose: This study aimed to assess the impact of segment-specific physical activity (PA) recommendations during the school day on the daily PA in both boys and girls. Methods: A total of 426 Czech and 219 Polish adolescents participated in this study. They were divided into two groups: one receiving segment-specific PA recommendations for the school day and the other receiving general daily PA recommendations. The Youth Activity Profile questionnaire, the World Health Organization-5 Well-Being Index, and the wearable Garmin vívofit were used in the research. Results: The application of segment-specific PA recommendations during the school day was significantly associated with higher PA on school days. It also increased the odds of meeting the recommendations of 6,000 steps/day after school (odds ratio = 1.63, confidence interval [1.19, 2.24], p = 0.003) and 11,000 steps/day (odds ratio = 1.59, confidence interval [1.16, 2.18], p = 0.004) on school days. Conclusions: Segment-specific PA recommendations during the school day are effective and should be integrated into physical education curricula, comprehensive school PA programs, and broader school educational strategies.