In the last stage of rehabilitation, high-intensity interval training (HIIT) for improving physical fitness is appropriate for return-to-play; however, some youth athletes visit the rehabilitation center less frequently due to conflict with their distance to center, and academic schedule. We tested the effects of short-term low-frequency HIIT in 54 youth male soccer players, after dividing them into a low-frequency group (LFG, n = 27 players) and a high-frequency group (HFG, n = 27 players). Muscle mass and body fat were measured using a body composition test, and VO2peak and exercise duration were measured using a treadmill. Five sets of anaerobic peak power and fatigue were measured repeatedly using the Wingate test. To evaluate knee joint muscle function, 60°/s, 180°/s, and 240°/s were measured using the isokinetic muscle function equipment. HIIT sessions were conducted twice a week for LFG and five times a week for HFG for 4 weeks. In this study, Wilcoxon signed-rank test and Mann–Whitney U test were mainly used for analysis. Significant improvements in VO2peak, anaerobic peak power, and knee strength were observed after intervention in both groups (p < 0.05). In the post test, there were significant differences between groups in VO2peak (LFG, 56.4 vs. HFG, 57.1 mL/kg/min; p = 0.035), exercise duration (LFG, 972.3 vs. HFG, 990.4 s; p = 0.041), Wingate anaerobic peak power 5 sets (LFG, 606.3 vs. HFG, 629.3 Watt; p = 0.039), and muscle function test 240°/s (LFG, 68.5 vs. HFG, 70.2 Jouls; p = 0.010). However, neither group showed significant changes in body composition, such as muscle mass or body fat (p > 0.05). In conclusion, although it is a short-term training, the effect of HIIT was shown in the HFG as well as LFG. Although HFG improved physical fitness, significant improvement was also achieved in LFG. Therefore, in the last stage of rehabilitation, low frequency as well as high frequency HIIT would be an appropriate training method to improve physical fitness for youth soccer players.