Background The aim of this study was to compare the effects of small-sided games (SSGs) and running-based high-intensity interval training (HIIT) on the body composition and physical fitness of youth female soccer players. Methods This study followed a randomized parallel study design. Twenty-four female soccer players (age: 18.63 ± 2.36 years) were randomly allocated to two training groups (SSG, n = 12; and HIIT, n = 12). The training intervention had a duration of eight weeks, consisting of three training sessions per week. Players were assessed twice (pre- and post-intervention) for anthropometrics, vertical (countermovement jumps, CMJ; and drop jumps, DJ) and horizontal jumping (single, triple and crossover hop), sprinting (10- and 30-m), change-of-direction (COD), COD deficit and final velocity at 30–15 Intermittent Fitness Test (VIFT). A covariance analysis (ANCOVA) was used to determine differences between the groups in the effect on post-intervention by controlling for covariates (pre-intervention). The within-group analysis (time) was performed using a paired t-test, while the between-group analysis per assessment moment was performed using an independent t-test. Results The between-group analysis with ANCOVA revealed that there are no significant differences between the SSG and HIIT groups in the post-intervention for any outcome (p > 0.05). The within-group analysis revealed significant improvements in both the SSG and HIIT groups in CMJ (p < 0.05), single, triple and crossover hops (p < 0.05), RSI DJ 30-cm and RSI DJ 40-cm (p < 0.05), VIFT (p < 0.05) and COD (p < 0.05). Conclusions SSG and HIIT are both effective for improving vertical and horizontal jumping ability, change-of-direction, and aerobic capacity status measured at a progressive and intermittent multistage test in youth soccer players.