Soccer is a multifactorial sport, in which players are expected to possess well developed physical, psychological, technical, and tactical skills. Thus, the anthropometric and fitness measures play a determinant role and could vary according to the competitive level. Therefore, the present study aimed to verify differences in body composition and physical performance between two soccer team. 162 young soccer players (from the Under 12 to Under 15 age categories; age: 13.01 ± 1.15 years) of different competitive levels (elite—n = 98 and non-elite—n = 64) were recruited. Anthropometric characteristics (height, weight, lengths, widths, circumferences, and skinfold thicknesses (SK)), bioelectrical impedance, physical performance test as countermovement jump (CMJ), 15 m straight-line sprints, Yo-Yo Intermittent Recovery Test Level 1 (Yo-Yo), and 20 + 20 m repeated-sprint ability (RSA)) were carried out. In addition, Body mass index (BMI), body composition parameters (percentage of fat mass (%F), Fat mass (FM, kg), and Fat-free mass (FFM, kg)) and the areas of the upper arm, calf and thigh were calculated, and the Bioelectric Impedance Vector Analysis (BIVA) procedures were applied. In addition, a linear discriminant analysis was assessed to determine which factors better discriminate between an elite and non-elite football team. Many differences were observed in body composition between and within each football team’s category, especially in triceps SK (p < 0.05), %F (p < 0.05), and all performance tests (p < 0.01). The canonical correlation was 0.717 (F(7,128) = 19.37, p < 0.0001), and the coefficients that better discriminated between two teams were 15 m sprint (−2.39), RSA (1−26), suprailiac SK (−0.5) and CMJ (−0.45). Elite soccer team players present a better body composition and greater physical efficiency. In addition, BIVA outcome could be a relevant selection criterion to scout among younger soccer players.