Rinko rules
Remove the wheels or fold the bike, and pack it fully in a bike bag. Nothing should stick out.
Keep the bag under 250 cm in total and 30 kg. If it is over 160 cm, book a seat with an oversized baggage area.
With a Japan Rail Pass, seats with an oversized baggage area are included at no extra cost. Book them by scanning the QR code on your pass at a Shinkansen ticket machine or at any staffed JR desk. Get your Japan Rail Pass
On board
Place the bag behind the last row of seats and secure it so it cannot tip over. Avoid rush hour trains.