The universal design of public transportation is a crucial task worldwide, especially in aging societies. For this reason, public agencies and train operators have advocated for universal architectural design for train stations, for instance, installing elevators and designing step-free routes. However, the location of elevators is often decided on an ad-hoc basis, and wheelchair users are often forced to take unnecessary detours and collision risks. This is because few methodologies are available for making an integrated evaluation of spatial structure and wheelchair accessibility. This paper introduces an evaluation framework based on network analysis to evaluate wheelchair accessibility from the aspect of the spatial structure at train stations. Specifically, we first develop weighted network data that describe the spatial structure of train stations in detail to represent the mobility restrictions of wheelchair users and pedestrians. We next propose several indices to evaluate each station in terms of its wheelchair accessibility using these data: “reachable time indices,” which measure the time to the train doors from the ticket gate, and “level of path independence,” which describes the low risk of collisions on paths. This evaluation framework was applied to nine train stations in Tokyo, Japan, as case studies to examine the relationship between spatial structure and wheelchair accessibility. As a result, we found three important relationships. First, placing an elevator in the center of a platform narrows the range of the reachable times for wheelchair users. Second, the proximity of elevator doors to stairs or escalator entrances tends to increase the risk of collisions with pedestrians. Third, a wheelchair stairlift installed in place of elevators increases the minimum reachable time and increases the risk of collisions on designated paths. These insights will be useful for finding facilities that require improvement in the wheelchair accessibility of step-free routes.