Background: Understanding the internal load characteristics of the knee joint is essential for investigating unilateral knee injuries associated with running. This study examined the differences in the location and magnitude of von Mises stress in the internal structures of bilateral knee joints during the stance phase of gait following 10 km running at submaximal speeds. Methods: A healthy male recreational runner participated in this study. We employed a synergistic approach, integrating subject-specific knee joint angles, reaction forces, and moments derived from musculoskeletal modeling to inform and drive the finite element (FE) modeling of running. This methodology ensured a detailed and accurate representation of knee joint mechanics. The peak stresses of the bilateral knee menisci, tibial cartilage, and five main ligaments were quantified using a FE model during the stance phase. Results: The meniscus, tibial cartilage, anterior (ACL), posterior cruciate ligament (PCL), medial (MCL), lateral collateral ligament (LCL) and experienced larger loads in the non-dominant limb across most phases of stance. Additionally, fatigue elevated the peak loading on the non-dominant limb’s ACL, PCL, and LCL during the gait stance phase but diminished the load on these ligaments in the dominant knee joint. For Patellar ligament (PL), the non-dominant side showed maximal stress at initial contact, while the dominant side dominated during the remaining stance phases. Conclusions: This proof-of-concept substantially enhances our understanding of the impact of running-induced fatigue on bilateral knee loading. It provides a detailed analysis of factors leading to unilateral knee overload during extended running. These insights are essential in formulating targeted strategies to reduce injury risks.