The aim of this study was to compare the effects of jumping interval training (JIT) and running high-intensity interval training (HIIT) on the aerobic, anaerobic and jumping performances of youth female aerobic gymnasts. A randomized controlled study was conducted over an 8-week period, involving 73 youth female athletes (16.2 ± 1.3 years old) of aerobic gymnastics. The study comprised two experimental groups (JIT and HIIT) and a control group. Participants in the experimental groups engaged in two additional training sessions per week alongside their regular training regimen, while the control group followed their usual training routine. Before and after the intervention period, gymnasts were assessed for their performance in the countermovement jump test (CMJ), the specific aerobic gymnastics anaerobic test (SAGAT) and the 20-m multistage fitness test. Significant interactions time × group were found in SAGAT (p < 0.001; = 0.495), CMJ (p < 0.001; = 0.338) and 20-m multistage fitness test (p < 0.001; = 0.500). The time × group analysis post-intervention revealed significantly lower scores in SAGAT for the control group compared to the JIT (p = 0.003) and HIIT (p = 0.034). Additionally, significantly higher scores were observed for the JIT group in the CMJ test compared to the HIIT (p = 0.020) and control (p = 0.028) groups following the intervention. Finally, the 20 m multistage fitness test post-intervention revealed significantly lower scores for the control group compared to JIT (p < 0.001) and HIIT (p < 0.001). Both JIT and HIIT are recommended training strategies to adopt in aerobic gymnastics for significantly improving the aerobic and anaerobic performances of athletes. However, JIT may be particularly relevant to use as it offers additional benefits in improving vertical jumping performances.