Taking the Train – Rinko Bags
One can bring their bike on any train in Japan but the requirement is that it be put inside a bag (known as a rinkobukuro, 輪行袋). These “bags” largely have two types, those where both wheels need to be taken off and ones where only the front wheel needs to come off. For speed (and protecting the rear derailleur we tend to prefer the latter).
Generally speaking, while strictly speaking against the rules having the seat poking out is tolerated. However, JR Shikoku is known for being a stickler and insisting that the entire bike being covered and having to take the seatpost out and carrying it separately.

Check out Road Bike Rental Japan’s overview Video – https://www.youtube.com/watch?v=ebahQhLMi0o
There are two types of rinko bag, those that require removing of both wheels removed (and consequently makes the bike smaller) and those that require on the front wheel removed. Removing only the front wheel makes packing and unpacking the bike faster but also protects the rear derailleur from damange. All train companies accept both types of Rinko Bag.
Bike Box


Most people who bring their bike from abroad arrive at the airport with their bicycle in a box. Taking your bike on the train while still in the box is fine but most rail operators have a rule that the maximum size of luggage that can be brought into the train of the sum of all dimensions being 250cm and some train companies do measure the boxes. (the author has had the Haneda Airport Keikyu staff measure their bicycle box so some staff will measure it.)
Also be mindful that it may be very difficult to find a place on limited express trains to put the bike box that won’t be in the way for other passengers. (on regular trains it should be easy to be out of the way of the other passengers)
Train companies generally don’t like to have dollies or carts brought into their stations as well but something small can certainly be helpful in getting your bike in the box to the station.
Etiquette when riding trains
Trains in Japan are crowded in cities and Japanese is culture is all about avoiding causing trouble for others. If you must travel through the city in the morning of a week day, travel early before or after the rush hour.
Also, as bicycles do take up space, riding the first or last cars is good ettiquette. Additionally, the area in front of the cab can be a good place to put the bicycle down and not be in the way of others.
Recently, many trains also have more wheelchair spaces (some trains in every car) so if one aligns themselves with the wheel chair markings on the platform, these spaces can be a good place to put the bicycle in the train and not have to walk to the far end.

Taking your bike on the Tokkaido/Sanyo/Kyushu Shinkansen
The Tokkaido Shinkansen as well as the Sanyo/Kyushu shinkansen run across the backbone of Japan and connect some of the best places for cycling in Japan including, Tokyo, Osaka, Hiroshima, the Shimanami Kaido and others.

The Tokkaido Shinkansen Trains are built to accomodate the maximum number of people and consequently there is limited space for bicycles inside the train.
It’s a common misconception that to bring a bicycle onto the Tokkaido Shinkansen a reservation of an oversized baggage seat is required. This is not the case despite what people say on online forums. (As written in JR Tokai’s oversized bag rules sports equipment is explicity excluded) However, if you would like to use that space, a reservation is required.

Additionally, a bicycle is not to fit in just one of the luggage spaces (as the reservation is only the space behind one seat) so unless you travel with friends and book all the seats there is a good chance that someone else may have reserved the other portion of the oversized baggage area leaving you without enough space to put the bicycle.
The lesser known, large bag storage area in the deck of the train can be much more useful for bicycles. If ibe us sure to reserve the lower one, a bicycle can fit it front of it quite easily and there is good amount of space there so Wabisabi Recommends this space as well.

Additionally, the Tokaido Shinkansen has an extra wide corridor on Car 11 due to the multipurpose toilet which can be an easy space to put a bicycle, just be sure to make sure you have a seat nearby to be able to move in the even that somebody who requires the additional width boards the train.
“Cycle Trains”
There are some trains that are specifically designed for bicycles to be taken on as is. The number of these is increasing over time as countryside train operators look for ways to increase revenues.
B.B.Base
From Ryogoku Station (Eastern Tokyo) to various places in Chiba Chiba. Bicycles can be taken on as is and
JR’s B.B.Base website (English)

Other Trains
Some train operators allow users to take bicycles as is onto all or some portions of their network at some times.
However, these are generally not in urban areas but on local operators and change relatively frequently. The below website does a good job of bringing that information together (in Japanese).
https://train-colors.net/cycletrain/

Busses
Highway Buses
Busses can often be an option in getting bicycles to the airport or other destinations.
As a general rule it not possible to get anything but a small folding bicycle onto a highway bus in Japan.
Most busses to the airport will take bicycles if there is enough space underneath the bus. If there isn’t the bike will be the first thing to go. If the bike is in a box (rather than a bag) it makes it much easier to store under the bus. Also taking the bus at a less crowded time can also help.
Local Buses
It can be up to the descretion of the driver of the bus, but if the bus isn’t crowded and the bike is in a rinko bag, one can generally get their bicycle onto a local bus. This can be a live saver in the countryside if one has a mechanical issue
Bicycle Busses
Naruto Bridge Bus
There are no ferries or ways for a bicycle to cross from Awaji into shikoku so there is a bus company that is specially equpped to handle bicycles. They can handle bicycles with and without a bike bag (Bus Company Website, Japanese only)
Airplanes
Each airline has their own rules.
Both JAL and ANA will take bicycles in rinko bags as luggage free of charge.
While it can be nerve racking to trust a bicycle to an airline at a big airport in Japan, this author has done so mulitple times without issue and even with significant searching has not found a single case where a bicycle was significantly damaged by airline staff in Japan.