Bicycles, particularly the simple mamachari fixed-gear commuter with a wire basket on the front, are ubiquitous in suburban areas and drivers are very used to dealing with them. Drivers are more polite than almost anywhere else and cycling is a good option for getting around some cities, like Kyoto. Biking on sidewalks/pavements is illegal, but this rule is widely ignored.

In busy urban areas, you typically have to pay for bicycle parking. Every train station will have parking lots (駐輪場 churinjo) that charge per hour or per day. Watch out for No Bike Parking (駐輪禁止 churin-kinshi) zones: bikes left in these are likely to be physically removed and getting them back will be a huge, often expensive hassle.

Bike share programs exist, but require non-Japanese to jump through hoops. In particular, Docomo Cycle requires a Japanese phone number to register.

Long-distance cycling in Japan is gaining popularity. Easily the longest route is the Pacific Cycling Road running 1,200 km (750 mi) along the Pacific coast, completed in 2021. Some well-known routes include:

• Shimanami Kaido Bikeway — connects the main island of Honshu to Shikoku, and runs from Onomichi to Imabari, a distance of 70 km (43 mi).
• Akinada Tobishima Kaido — the less-known cousin of the Shimanami Kaido, from Kure to Imabari.
• Kibi Plains Cycling Route from Okayama to Soja.
• Hamanako Cycling Course around the lake in Hamamatsu.
• Tonegawa Cycling Road, stretches from Gunma Prefecture through Saitama Prefecture all the way to the Pacific Ocean, totaling 170 km (110 mi).
• Yamanobe-no-michi, possibly Japan's oldest road, running from Sakurai near Nara to Tenri on the outskirts of Osaka.

All of these have bike rental facilities and detailed information available, although often only in Japanese.

An excellent series of maps are called "Touring Mapple". They are produced for Japanese motorcycle tourists, but have a great deal of useful information for bicycle tourists. They list scenic routes, campgrounds, hostels, and numerous minor roads. As they are Japanese language they are of limited use for general navigation for those without some Japanese reading skills, however they can be quite useful when supplemented with an English (or romaji) map. Translations of the index are available online.

Nearly every large city and many small cities have bike rentals, called Rent-a-cycles (レンタサイクル rentasaikuru), usually for half-day/one-day (around ¥500/1000 is typical). Many shops only do single-day rentals, and often the only option is the fixed-gear mamachari. Electric bikes (電動アシスト dendō assist) are increasingly available, but this is typically just a motorized mamachari. Japanese rules restrict electric bikes to pedal assist only with 250W max and a top speed of 24 km/h (15 mph).

In areas with well-known and popular cycling routes, there are certain to be places to rent bicycles, so it is not necessary to bring a bike to Japan unless you are planning more original routes or traveling across country. Some places, like the aforementioned Shimanami Kaido and Kibi Plains Cycling Route allow you to rent a bike at one end and return it at the other end. If you're allowed to leave your bike at a designated point instead of returning it (乗り捨て norisute, lit. "ride and throw away"), you're often charged an additional fee compared to bringing it back to your starting point (店舗返却 tenpo henkyaku).

Basic mamachari-type bikes can be picked up in Japanese superstores including Don Quijote or Aeon for as little as ¥10,000. For more serious bicycles, known in Japan as "sports cycles" (スポーツサイクル), look for a specialist bike shop (自転車屋さん jitenshaya-san). The oddly named Y's Road is Japan's largest chain with stores nationwide, and is more used to dealing with tourists than the average corner shop.

The main wrinkle with buying a new bike in Japan is that bike registration (自転車防犯登録 jitensha bōhan tōroku) is mandatory, and while this does not require a Japanese ID, you are supposed to provide an ID with a Japanese address, which is going to be difficult for a casual tourist to pull off. The laws don't really specify how non-residents are supposed to be handled, so some places will happily register you at a random Japanese address like your hotel, while others will refuse point blank.

If you purchase a new bike at a bike shop, they can sort out registration for you. If you purchase or receive a bike from a friend, or get a second-hand bikes, be sure to get a certificate of transfer (自転車譲渡証明 jitensha jōto shōmei) that you can bring to a police station for the registration. A fee of ¥500 or so applies.

Bike liability insurance (自転車保険 jitenshahoken) is required in 34 (out of 47) prefectures as of April 2024.

Don't try to ride a bicycle that's registered to someone else: it is considered stolen in Japan, and you will likely be taken to the police station. The police often does check, so avoid problems by obeying the law.

While all bikes in Japan are supposed to be registered, there is no legal penalty for not registering a bike, nor is there any obvious process for registering a non-Japanese bike, and this little loophole makes it feasible to import your bike from overseas. Police registration checks target sketchy characters on commuter bikes, not the type of bike that's worth importing (road bikes etc). In the unlikely event that you are stopped, showing your passport plus ideally a copy of your overseas purchase receipt should suffice to prove it is, indeed, your own bicycle and not stolen.

Transporting bikes long distances in Japan can be pain. Usually trains only allow bikes in a "rinko bag" (bike bag, 輪行袋 rinkō-bukuro or 輪行バッグ rinkō baggu). This requires a folding bicycle or removing one or both wheels, so it's not very convenient for short trips. Rinko bags can be purchased at any bike shop, and ultralight ones that pack small (but provide very little protection) are also available.

Long-distance buses often don't allow bicycles, and on local buses it may be at the driver's discretion; in both cases, a rinko bag would also be required. Don't go during busy commuting hours, pack your bicycle away from the station, keep things clean (bicycle, bag, and your hands), and don't take up too much space or impede other passengers. Booking a seat at the back of long-distance trains near the storage areas may be helpful. Ferries allow bicycle for a small fee.

Courier services can ship bicycles anywhere across the country, but since bicycles are large and bulky, the cost is also considerable, often north of ¥10,000. You will also need a cardboard box to pack the bicycle into, a rinko bag will not cut it.

Japan has strict biking laws. Bicycling while distracted (such as by using or looking at a mobile phone while moving) could result in a fine of up to ¥100,000 or up to six months in jail, with increased penalties if distracted biking results in an accident. Cycling while drunk (blood alcohol level of at least 0.15 mg/L) could result in up to three years in prison or a fine of up to ¥500,000.

Children, by law, must wear helmets. In addition, helmets for adults became a "duty of effort" in 2023; in other words, there are no immediate penalties but you will be in a very bad position in case of accidents. Lights are also mandatory if cycling at night.