Orthopedic complications were previously reported for patients with increased femoral anteversion. A more comprehensive analysis of the influence of increased femoral anteversion on joint loading in these patients is required to better understand the pathology and its clinical management. Therefore, the aim was to investigate lower-limb kinematics, joint moments and forces during gait in adolescent patients with increased, isolated femoral anteversion compared to typically developing controls. Secondly, relationships between the joint loads experienced by the patients and different morphological and kinematic features were investigated. Patients with increased femoral anteversion (n = 42, 12.8 ± 1.9 years, femoral anteversion: 39.6 ± 6.9°) were compared to typically developing controls (n = 9, 12.0 ± 3.0 years, femoral anteversion: 18.7 ± 4.1°). Hip and knee joint kinematics and kinetics were calculated using subject-specific musculoskeletal models. Differences between patients and controls in the investigated outcome variables (joint kinematics, moments, and forces) were evaluated through statistical parametric mapping with Hotelling T2 and t-tests (α = 0.05). Canonical correlation analyses (CCAs) and regression analyses were used to evaluate within the patients’ cohort the effect of different morphological and kinematic predictors on the outcome variables. Predicted compressive proximo-distal loads in both hip and knee joints were significantly reduced in patients compared to controls. A gait pattern characterized by increased knee flexion during terminal stance (KneeFlextSt) was significantly correlated with hip and knee forces, as well as with the resultant force exerted by the quadriceps on the patella. On the other hand, hip internal rotation and in-toeing, did not affect the loads in the joints. Based on the finding of the CCAs and linear regression analyses, patients were further divided into two subgroups based KneeFlextSt. Patients with excessive KneeFlextSt presented a significantly higher femoral anteversion than those with normal KneeFlextSt. Patients with excessive KneeFlextSt presented significantly larger quadriceps forces on the patella and a larger posteriorly-oriented shear force at the knee, compared to patients with normal KneeFlextSt, but both patients’ subgroups presented only limited differences in terms of joint loading compared to controls. This study showed that an altered femoral morphology does not necessarily lead to an increased risk of joint overloading, but instead patient-specific kinematics should be considered.