Background/ObjectiveThis study was conducted during the 2019–2020 academic year to evaluate the impact of participation in school sports on students’ Body Mass Index (BMI) and Assessing Levels of Physical Activity (ALPHA) test scores. Interrupted by the COVID-19 pandemic, which led to a suspension of in-person education, the study resumed in September 2021, refocusing on the effects of pandemic-induced inactivity on the physical fitness levels of the same cohort.MethodsThe study included twenty-nine male high school students (age: 17,24 ± 0,73 years), divided into thirteen athletes (participating in sports such as football, basketball, and track) and sixteen non-athletic counterparts. They underwent reassessment using the ALPHA test battery, evaluating cardiorespiratory, musculoskeletal, and motor skills fitness. Data were analyzed using independent and paired samples t-tests and a two-way repeated measures ANOVA to assess changes over time and between groups. Discriminant function analysis evaluated the ALPHA test’s ability to classify students based on their athletic status pre- and post-pandemic.ResultsInitially, athlete students exhibited significantly better BMI, 20 m shuttle run, and 4 × 10 m speed run scores compared to their non-athlete peers. After the pandemic, only the 20 m shuttle run scores remained significantly higher for athletes, with diminished distinctions in other fitness areas. The classification accuracy of the ALPHA test battery decreased from 89.7 to 75.9% post-pandemic.ConclusionThe enforced sedentary lifestyle due to the COVID-19 pandemic adversely affected all students, particularly diminishing health-related fitness parameters such as body composition, cardiorespiratory and musculoskeletal strength, and motor skills. Students previously engaged in regular physical activity, notably school athletes, experienced significant fitness declines. This highlights the urgent need for targeted interventions to encourage active lifestyles among youth in the post-pandemic phase, aiming to avert long-term adverse health outcomes.