Team handball is a highly dynamic sport where physical demands differ between categories and roles. Thus, physical characteristics are fundamental for the final performance. This study aims to (a) characterize a sample of young male and female elite team handball players with a non-athletic reference population; (b) to generate their 50%, 75%, and 95% percentiles of the bioelectrical variables. The study included 55 young elite team handball players (Males, n = 37, age = 17.0 ± 1.2 yrs, height = 185.8 ± 7.3 cm, weight = 82.0 ± 11.0 kg, body mass index (BMI) = 23.7 ± 2.5; Females, n = 18, age = 17.8 ± 0.9 yrs, height = 171.2 ± 6.4 cm, weight = 67.4 ± 7.2 kg, BMI = 23.0 ± 2.0). Height and bioelectrical variables were assessed in a state of euhydration and standard conditions. Bioelectrical impedance vector analysis (BIVA) was used to characterize the bioelectrical vector (BIA vector) distribution pattern for each group. Compared to the reference values, BIA vector showed statistically significant differences in males U17 (n = 19, T2 = 51.0, p < 0.0001), males U19 (n = 18, T2 = 82.0, p < 0.0001) and females U19 (n = 18, T2 = 85.8, p < 0.0001). Male groups were also bioelectrically different (T2 = 13.7, p = 0.0036). BIVA showed specific bioelectrical characteristics in young male and female elite handball players. This study provides an original data set of bioelectrical impedance reference values of young male and female elite team handball players. Our result might help to interpret individual bioimpedance vectors and define target regions for young handball players.