Background and Objectives: This study aimed to investigate the magnitude of vertical jump inter-limb asymmetries among young highly-trained basketball athletes and to analyze its impact on sport performance, specifically in sprints, agility, and vertical jumps. Materials and Methods: A unilateral countermovement jump (CMJ) was employed to determine Inter-limb Index Asymmetry (IAI) in 320 participants aged from 14 to 18 years, from the Valencia Basket youth academy. IAI was categorized into three groups: 0–9.9%, 10–14.9%, and >15%. The relationship between IAI and performance variables was analyzed through correlation studies (Pearson or Spearman’s). The influence of IAI magnitude was assessed using ANOVA or Kruskal–Wallis analysis, with leg dominance as a covariable. SPSS Statistics version 26 was used for analysis. Results: Among all the participants, the mean IAI was 10.6%. Correlation studies revealed non-significant values (p < 0.05) between IAI and sport performance variables. The three IAI magnitude groups did not show statistically significant differences in sprint, agility, and jump outcomes. Leg dominance did not seem to influence performance outcomes, except for unilateral CMJ. Conclusions: The results obtained challenge the assumption that an IAI above 10% negatively affects sprint, agility, or jump performance in young basketball athletes. Notably, the magnitude of IAI did not influence sport performance parameters, suggesting that the 10–15% threshold from previous studies may not be applicable to this population. The study emphasizes the need to understand lower-limb asymmetries in the context of specific sport task performance, considering the potential evolution over time among affected young athletes.