The aim of the study was to determine the effect of coronavirus disease (COVID-19) on the physical fitness of children aged 16, living in Kosovo. The research was conducted on a sample of 41 students aged 16 years ± 6 months, who are high school students from the Republic of Kosovo (n = 41 boys). Physical tests included in the study to measure the anthropometric and motor abilities included, height, weight, body mass index, balance, flexibility, strength continuity, explosive force, and anaerobic peak power. The calculation of the data was made by using the SPSS 24 software program. The One-Way repeated measure ANOVA Analysis was used to calculate the statistical data of the tests that were included in the study (years: 2018, 2019, and 2020). The study results have shown statistically significant effects of the pandemic on motor abilities, such as on explosive force and anaerobic peak power. However, there is no significant effect of the pandemic on anthropometric characteristics, balance, and flexibility (p>0.05). The effects of the pandemic on the health of the children living in Kosovo were less in comparison with the effects of the pandemic reported by the World Health Organization and other countries. Moreover, the study also showed decreases in motor abilities in the years when the COVID-19 pandemic had not occurred.