Digital anthropometry by three-dimensional optical imaging systems and smartphones has recently been shown to provide non-invasive, precise, and accurate anthropometric and body composition measurements. To our knowledge, no previous study performed smartphone-based digital anthropometric assessments in young athletes. The aim of this study was to investigate the reproducibly and validity of smartphone-based estimation of anthropometric and body composition parameters in youth soccer players. A convenience sample of 124 male players and 69 female players (median ages of 16.2 and 15.5 years, respectively) was recruited. Measurements of body weight and height, one whole-body Dual-Energy X-ray Absorptiometry (DXA) scan, and acquisition of optical images (performed in duplicate by the Mobile Fit app to obtain two avatars for each player) were performed. The reproducibility analysis showed percent standard error of measurement values < 10% for all anthropometric and body composition measurements, thus indicating high agreement between the measurements obtained for the two avatars. Mobile Fit app overestimated the body fat percentage with respect to DXA (average overestimation of + 3.7% in males and + 4.6% in females), while it underestimated the total lean mass (− 2.6 kg in males and − 2.5 kg in females) and the appendicular lean mass (− 10.5 kg in males and − 5.5 kg in females). Using data of the soccer players, we reparameterized the equations previously proposed to estimate the body fat percentage and the appendicular lean mass and we obtained new equations that can be used in youth athletes for body composition assessment through conventional anthropometrics-based prediction models.