This project aims to recognize the school experiences of Polish students during the COVID-19 outbreak; we focused on the area of assessment of physical well-being and leisure time. Nearly two thousand primary or secondary school students aged 9 to 20 participated in the survey. Running descriptive statistics, frequency analysis, and significant difference tests, we found that 45% of students thought their physical well-being during the COVID-19 outbreak worsened compared to pre-pandemic times. Boys declared they felt better in their physical well-being than girls (p < 0.001). Most students noticed changes in the quality of their leisure time activities; boys were happier than girls in their free time during the outbreak (p < 0.001). Learners’ ages also differentiated the assessment of their physical well-being (p < 0.001) and leisure time (p < 0.001). The youngest students more often assessed their experiences in the researched fields as good or increased, while the older groups more often noticed a decrease. Multinomial logistic regression proved that the differences in the assessments of physical well-being and leisure time could be explained to the greatest extent by age and gender, whereas the place of residence and school location were insignificant. All in all, our study confirms the dominance of the adverse effects of the COVID-19 pandemic on physical well-being and changes in leisure time. As such, it is advisable (during and after outbreaks) to support children and adolescents by targeting individual and institution levels. We recommend developing techniques to reduce stress and information overload, increasing creative ways of spending leisure time, supporting families in navigating children’s free time, and expanding social support networks.