Rail transport in Japan is a major means of passenger transport, especially for mass and high-speed travel between major cities and for commuter transport in urban areas. It is used relatively little for freight transport, accounting for just 0.84% of goods movement. The privatised network is highly efficient, requiring few subsidies and running with extreme punctuality, though since privatisation several unprofitable but socially valuable lines have been closed by private operators.

Rail transport services in Japan are provided by more than 100 private companies, including

• Six Japan Railways Group (JR) regional companies (state owned until 1987) which provide passenger services to most parts of Hokkaido, Honshu, Shikoku and Kyushu; 
• The nationwide JR freight company; and
• 16 major regional companies which provide railway services as part of their corporate operations. There are also dozens of smaller local private railways.

Many of the private rail companies rank among the top corporations in the country. Railways were built by private corporations developing integrated communities along the railway lines, allowing them to achieve profitability by diversifying into real estate, retail, and numerous other businesses. These rail integrated communities are a form of transit-oriented development unique to the rail system in Japan. Rail integrated communities increase walkability in these urban spaces. As they are to be used by pedestrians, they include sidewalks and bikeways. Regional governments, and companies funded jointly by regional governments and private companies, also provide rail service.

There are 30,625 km (19,029 mi) of rail crisscrossing the country. JR (a group of companies formed after privatization of JNR) controlled 20,135 km of these lines as of March 31, 1996, with the remaining 7,133 km (4,432 mi) in the hands of private enterprise local railway companies. Japan's railways carried 9.147 billion passengers (260 billion passenger-kilometres) in the year 2013–14. In comparison, Germany has over 40,000 km (25,000 mi) of railways but carries only 2.2 billion passengers per year. Because of the massive use of its railway system, Japan is home to 46 of the world's 50 busiest stations.

Japan pioneered the high-speed shinkansen or "bullet train", which now links Japan's largest cities at speeds of up to 320 km/h (200 mph). However, other trains running on the conventional line or "zairaisen" remain relatively slow, operating at fastest 160 km/h (99 mph) and mostly under 130 km/h (81 mph), most likely due to the wide usage of Narrow-gauge tracks they operate on.