This study presented a systematic review of recent advancements in the application of finite element (FE) methods to running and running shoe biomechanics. It focused on outlining the general approach to build foot-running shoe FE models, exploring their current applications and challenges, and providing directions for future research. The review also aimed to highlight the gap between theoretical mechanical responses in simulations and real-world manifestations of running-related musculoskeletal injuries (RRMI). A comprehensive search of electronic databases, including Web of Science, PubMed, and Scopus, identified 12 eligible articles for inclusion in this review. Current studies have examined the effects of various running shoe design features and conditions on the mechanical response of internal foot tissues using foot-running shoe FE models. These models have gradually evolved from simplified local representations to more realistic and comprehensive models, with the incorporation of experimental data enhancing simulation accuracy. However, to further improve simulation outcomes, key advancements are proposed to reduce development time and enhance model robustness. These include high-fidelity 3D model development, personalized shape transformation, AI-driven automated reconstruction, comprehensive dynamic running simulations, and improved validation methods. More importantly, future research needs to bridge the gap between FE simulations and RRMI risk by addressing the complexities of bone fracture criteria and conducting localized assessments of bone properties. Overall, this review provided valuable insights for biomedical engineers, medical professionals, and researchers, facilitating more accurate investigations of foot-running shoe FE models. Ultimately, these advancements aim to improve footwear design and training programs to reduce the risk of RRMI.