If your trip is more than a week, it might be better to get a Japan Rail Pass (JR Pass) to save you time and money.
Official Price Table (Price unit: JPY)
- 1 week stay in Japan, Using Narita airport
- Staying near Shinjuku in Tokyo
- Short trip to Kyoto from Tokyo
- JR Pass (Ordinary): 29,110 JPY
- Round trip bullet train ticket (Shinkansen) to Kyoto: 26,160 JPY + Round trip Narita Express ticket from Narita airport to Shinjuku 6,380 JPY
Obviously, the JR Pass is cheaper in this case. You can also enjoy unlimited free JR transportation during your trip in Tokyo and Kyoto without needing to buy tickets for each ride.
I recommend you make a rough estimate of your planned long distance transportation. In most cases, JR Pass would be cheaper for stays over one week.
If you need help calculating the cost, please leave a comment with your basic plan.