The aim of this study was two-fold: (i) to compare physical fitness adaptations following small-sided games (SSG) and running-based high-intensity interval training (HIIT), considering sex interactions; and (ii) to describe intra-individual variations of adaptations in both men and women developmental/trained soccer players over an 8-week randomized parallel study design involving 25 women and 27 men. Pre and post-intervention assessments included countermovement jump (CMJ), 10-meter linear sprint test, change-of-direction (COD) deficit, and final velocity at 30-15 Intermittent Fitness Test (VIFT). Significant interactions between time, groups and sex were found in 10-m sprint (F_1,48 = 6.042; p = 0.018; η_p² = 0.112). No significant interactions between time, groups and sex were found in CMJ (F F_1,48 = 0.609; p = 0.439; η_p² = 0.013), COD deficit (F F_1,48 = 2.718; p = 0.106; η_p² = 0.054) and VIFT (F F_1,48 = 1.141; p = 0.291; η_p² = 0.023). Significant interactions were found between time and sex in CMJ (F F_1,48 = 29.342; p < 0.001; η_p²= 0.379), 10-m sprint (F F_1,48 = 4.359; p = 0.042; η_p² = 0.083), COD deficit (F F_1,48 = 5.066; p = 0.029; η_p²= 0.095) and VIFT (F F_1,48 = 11.248; p = 0.002; η_p² = 0.190). In conclusion, this study suggests similar effects of HIIT in both sexes. However, for women, SSG may entail less efficacy and more inter-individual variability compared to men. Therefore, HIIT could potentially be a better solution for women, whereas both training approaches were equally effective in men.