By train: Japan's efficient rail network makes travelling by train a good option. High-speed bullet trains run between Tokyo and Kyoto in less than 3 hours; while the Osaka to Kyoto trip takes only 30 minutes. Slower trains are also available and considerably cheaper; however, they don't always run direct and may involve transfers.
By bus: long-distance buses are a good option if you want to save money. There are many departures and arrivals both day and night, serving major cities throughout Japan. Several private companies offer a choice of routes including the JR Bus Group that has a service to Tokyo, taking 8 hours.