The aims of the present study were (i) identify and compare the basic anthropometric characteristics, motor performance, game-related skills and functional capacity of under-15 (U-15) and under-16 (U-16) male basketball players, (ii) examine the influence of maturity offset on all performance parameters, (iii) predict test outcome in linear speed, agility, jumping, aerobic endurance and sport-specific skills. Two hundred thirty-four athletes volunteered participated in the study and completed a test battery including morphological variables (body height, body mass, standing reach), fitness (agility, jumping performance, aerobic endurance), technical skills (jump shot, free throws, dribbling) and functional movement screen. The U-16 group outperformed U-15 in terms of body height and mass, but also SVJmax and VJmax. Moreover, when data was adjusted considering chronological age, the group with more advanced maturity offset within U-15 group had achieved greater values in body mass, body height, arm reach and VJmax variable. Data analysis adjusted for age, body height and body mass with the reference to years after PHV showed that PHV2 group among U-15 basketball players had better jumping performance, and 20 m linear speed compared to PHV1 group. Maturity status was a relevant predictor of 20 m linear speed and SVJ tests. Other results indicate that chronical age (20 m speed, VO2max), body height (5, 10, 20 m speed, agility), body mass (agility), functional abilities (20 m speed, SVJ, VJ, VO2max) were significant predictors of physical performance. On the other hand, only body height (free throws) and FMS (jump shot, dribbling) manifested an impact on the level of sport-specific skills. The obtained results indicate that FMS test applied to young basketball players is not only right tool for injury prediction but also its outcome can influence technical performance. Therefore, we can conclude that composite score of < 14 out of 20 may result in low level of sport-specific capacity. It is significant evidence of practical application of FMS tests.