This study investigated the hierarchical structure of physical characteristics in elite young (i.e., U17-U19) basketball players according to playing positions. In addition, their predictive value of physical characteristics was determined for the evaluation of players’ physical preparedness. Sixty elite male basketball players performed 13 standardized specific field tests in order to assess the explosive power of lower limbs, speed, and change-of-direction speed. They were divided into three groups according to playing positions (guard [n = 28], forward [n = 22], center [n = 10]). The basic characteristics of the tested sample were: age = 17.36 ± 1.04 years, body height = 192.80 ± 4.49 cm, body mass = 79.83 ± 6.94 kg, and basketball experience = 9.38 ± 2.10 years for guards; age = 18.00 ± 1.00 years, body height = 201.48 ± 3.14 cm, body mass = 90.93 ± 9.85 kg, and basketball experience = 9.93 ± 2.28 years for forwards; and age = 17.60 ± 1.43 years; body height = 207.20 ± 3.29 cm, body mass = 104.00 ± 9.64 kg, and basketball experience = 9.20 ± 1.62 years for centers. For all playing positions factor analysis extracted three factors, which cumulatively explained 76.87, 88.12 and 87.63% of variance, respectively. The assessed performance measures were defined as significant (p < 0.001), with regression models of physical performance index (PPINDEX). PPINDEX of guards = −6.860 + (0.932 × t-test) − (1.656 × Acceleration 15 m) − (0.020 × Countermovement jump); PPINDEX of forwards = −3.436 − (0.046 × Countermovement jump with arm swing) − (1.295 × Acceleration 15 m) + (0.582 × Control of dribbling); PPINDEX of centers = −4.126 + (0.604 × Control of dribbling) − (1.315 × Acceleration 15 m) − (0.037 × Sargent jump). A model for the evaluation of physical performance of young basketball players has been defined. In addition, this model could be used as a reference model for selection procedures, as well as to monitor the efficacy of applied training programmes within the short, medium and long-term periodization.