This study aimed to verify whether a group of young well-trained basketball players presented deficiencies in vitamin D concentration, and to analyze whether there was an association between vitamin D concentration and jumping and hopping performance. Gender differences were considered. Twenty-seven players from an international high-level basketball club (14 female, 16.00 ± 0.55 years; 13 male, 15.54 ± 0.52 years) participated in this cross-sectional study. Rate of force development was evaluated by means of the Abalakov test (bilateral: AbB; right leg: AbR; left leg: AbL); and the triple hop test (right leg: THR; left leg: THL). Blood samples were collected for the determination of serum 25-hydroxyvitamin D and nutritional status. Vitamin D insufficiency was found in both women (29.14 ± 6.08 ng/mL) and men (28.92 ± 6.40 ng/mL), with no gender differences regarding nutritional scores. Jumping and hopping performance was confirmed to be significantly larger in males (AbL, THR, and THL p < 0.005), whose CV% were always smaller. A positive correlation was found between AbB and vitamin D (r = 0.703) in males, whereas this correlation was negative (−0.611) for females, who also presented a negative correlation (r = −0.666) between THR and vitamin D. A prevalence of hypovitaminosis D was confirmed in young elite athletes training indoors. Nutritional (i.e., calciferol) controls should be conducted throughout the season. Furthermore, whilst performance seems to be affected by low levels of this vitamin in men, these deficiencies appear to have a different association with jumping and hopping in women, pointing to different performance mechanisms. Further studies accounting for differences in training and other factors might delve into these gender differences.