Hydrogen fuel cell trains (HFCTs) offer a clean and sustainable alternative to conventional rail transport, yet their large-scale implementation is restricted by inadequate hydrogen refueling infrastructure. This paper analyzes the current development status and major challenges in the layout of hydrogen refueling stations (HRSs) for rail transit. It highlights the lack of coordination between station siting and railway line planning, leading to mismatched infrastructure and inefficient resource allocation. Additionally, low train operation density results in underutilized stations and prolonged return on investment. Technological immaturity in liquid hydrogen storage and transportation further limits station flexibility and increases operational risks. The study suggests integrated planning across energy and transport networks, financial incentives, and technological innovation—particularly in liquid hydrogen logistics—to enhance the efficiency, safety, and economic viability of hydrogen-powered rail systems.