This retrospective study aimed to estimate the differences between selected indicators of physical fitness and body composition in young tennis players during the COVID-19 pandemic (2020 and 2021) and their values as predicted using the pre-pandemic trend (2015–2019). Data were collected from selected boys (mean ± SD; 13.2 ± 1.7 years) and girls (13.1 ± 1.9 years) during annual tests. Data were analyzed with linear mixed-effects models for males and females, separately, to predict body composition and physical fitness test scores, adjusting for age and pre-pandemic trends in the data. Compared with expected values, body fat mass increased in boys (2020: 0.68; 0.44–0.92, 2021: 1.08; 0.72–1.43), whereas muscle mass decreased (2020: −0.22; −0.34–−0.10, 2021: −0.28; −0.46–−0.10) throughout the pandemic. Interestingly, boys’ age-adjusted squat jump test scores improved relative to their expected scores during COVID-19 (2020: 0.19; 0.00–0.38, 2021: 0.35; 0.06–0.63). No other differences between predicted and measured values were noted across the observation period. The results of this study suggest that the sustained reduction in sports activity caused by the pandemic may have negatively affected the body composition of athletes; however, this did not affect selected performance indicators.