If you are new to Japan and have a car, one thing that you need to know is that highways (expressways)  are not free to use.  They are all toll roads.  In exchange for your hard-earned yen, you get the privilege of a higher speed limit, two lanes to work with, and no stoplights.  It can cut travel time dramatically–it’s as much as 400% faster.

Generally, tolls are done like parking tickets:  you take a ticket and then pay when you exit.  A few toll roads (for example, the Kyuragi toll road between Taku and Karatsu) require you to pay a fixed toll as you enter. But generally, it is ticket-based.

Nexco (Nippon EXpressway COrp.), the company that  runs the tolls roads, has this website in English that can give you information on using the expressways.

http://global.c-nexco.co.jp/toll/methods.html