As automated warehouses become increasingly central to modern supply chains, driven by evolving consumer demands, the durability and safety of rack structures, particularly shuttle rails, are becoming more critical than ever. These critical components are subjected to repetitive loading cycles as shuttles transport goods, making them susceptible to fatigue-related failures. Despite the importance of fatigue in these applications, traditional rack sizing methods often neglect fatigue considerations, primarily focusing on static load-bearing capacity. When fatigue is assessed, the evaluations typically center around Mode I failure, which considers normal stress-induced cracking. However, this approach fails to account for the more complex triaxial stress states and Mode III shear fatigue that occur particularly in the joints between rails—areas where stress concentrations and multiaxial loading are prevalent. To address this gap, this study evaluates the potential and limitations of both traditional and multiaxial fatigue procedures in capturing the effects of complex stress states on the fatigue performance of shuttle rails. This evaluation is conducted through a detailed numerical analysis of a real-world case study. The research underscores the critical need to incorporate multiaxial fatigue methods in the design and assessment of shuttle rails. Relying solely on traditional fatigue calculations can overestimate the actual fatigue life of these components, potentially compromising the safety and functionality of automated storage systems. By analyzing the complex relationship between different fatigue modes and stress states in rail joints, this research uncovers key insights into possible failure mechanisms during operation. The study emphasizes the importance of adopting more comprehensive fatigue evaluation techniques to ensure the reliability of rack structures in high-throughput automated warehouses over time.