The effects of railway operation on soil environments are an important topic. In this research, soil samples were collected from two diesel-driven railways and two electric railways in Japan. A positive matrix factorization (PMF) model was applied to investigate the sources of eight heavy metals in the soil near the railways. The results showed that railway operation was the dominant anthropogenic source of heavy metals in the soil in the study areas among five potential sources, with contributions ranging from 11.73% to 42.55%. Compared with that of electricity-driven railways, the effect of diesel-driven railways was larger. The environmental risk-assessment analysis suggested that the soils near the selected railways fall within the weak-to-extremely strong contamination category, and experienced moderate-to-extremely strong ecological risk. A health risk assessment revealed that the soil presented both noncarcinogenic and carcinogenic risks for children, with ingestion as the principal exposure pathway. The PMF-Environment Risk Assessment and PMF-Human Health Risk Assessment models were developed to obtain the ecological and human health risks for every source category. Railway operation was regarded as the major factor influencing ecology and human health at the diesel-driven railway sampling sites. However, at electricity-driven railway sampling sites, natural sources were dominant.