The aim of this study was to analyse sex-specific differences contributing to dynamic valgus in competitive soccer players before and after a standardised fatiguing protocol. Thirty-nine healthy female and male competitive soccer players (19 females and 20 males) were recruited for the purpose of this study. Bilateral medial knee displacement (MKD) was assessed during drop jump landings using a three-dimensional motion capture system before and after a standardised fatiguing protocol. In addition, all soccer players underwent clinical examinations, including rotational hip range of motion (ROM), isokinetic strength testing and magnetic resonance imaging (MRI) of the hip and knee. Sex-specific and fatigue-dependent differences were reported, and the influence of demographic, clinical and radiographic factors on MKD was analysed via multiple linear regression models. Compared with male soccer players, female soccer players demonstrated a tendency towards increased MKD during drop jump landings before (p = 0.09) and after the fatiguing protocol (p = 0.04). Sex-specific differences included increased hip internal rotation (IR) ROM, decreased hip external rotation (ER) strength and increased femoral torsion in females (all p < 0.002). According to the multiple linear regression models (stepwise method), increased hip IR ROM (90° of flexion) and the non-dominant leg remained the sole independent predictors of increased MKD during drop jump landings before (p < 0.01 and p = 0.02, respectively) and after fatigue (p < 0.01 and p < 0.01, respectively). An increase in hip IR ROM in females was linearly related to MKD after fatigue (R2 = 0.25; p < 0.01). Female soccer players exhibited increased dynamic valgus before and after fatigue, which is likely attributed to joint mobility, as well as muscular and anatomical differences, such as increased hip IR ROM, reduced hip ER strength and increased femoral torsion. In particular, females with increased hip IR ROM were more susceptible to effects of fatigue on MKD, which may increase their risk for anterior cruciate ligament injury. Level III.