Supplementary high-intensity interval training (HIIT) programs, focusing on different aspects of fitness, are commonly used in soccer practice. This study examined the impact of two different HIIT formats applied during the competitive season on aerobic and neuromuscular performance. Twenty-six young players from two youth amateur soccer teams (aged 18.1 ± 0.7 and 18.7 ± 1.1 years) participated. In a randomized design, Team A served as an experimental group, performing either a 10s/10s linear running HIIT or a 15s/15s HIIT with changes of direction, both at 100% of maximum aerobic speed, twice per week for six weeks. In that period, team B acted as a control group, maintaining their usual training soccer regimen. Following two weeks of lower volume and frequency training, team B added the two HIIT formats in their training for six weeks, while team A acted as control. Before and after each 6-weeks period, aerobic fitness and neuromuscular performance was evaluated by the countermovement jump (CMJ). The 3-way ANOVA showed that both HIIT formats significantly enhanced Yo-Yo Intermittent Recovery Test Level 1 (Yo-YO IR1) performance compared to the respective control periods. However, the main finding was that the 10s/10s compared with the 15s/15s HIIT format induced 45-50% greater improvements in Yo-YO IR1 (total distance: 18.5 ± 11.7% vs. 9.0 ± 8.5%, V̇O2max: 5.6 ± 3.2% vs. 3.0 ± 2.7%, and vV̇O₂max: (3.3 ± 1.9% vs. 1.8 ± 1.7%, all p = 0.39, d = 0.85). Countermovement jump performance remained unchanged across both groups (p > 0.68). During HIIT rating of perceived exertion was higher in the 15s/15s vs. the 10s/10s format (6.4 ± 0.5 vs. 4.7 ± 1.2 a.u., p < 0.001). These findings suggest that while both HIIT formats effectively enhance aerobic performance during the season, the 10s/10s format offers superior benefits with less perceived exertion, while the 15s/15s format induces higher internal load.