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I am debating taking a job in Japan. I have a ~11kg dog, and want to get a sense of how hard it would be to travel with her.

For example, would she be allowed on the Narita Express to Tokyo? Or on any of the local trains around the Tokyo area? If I wanted to travel on the weekend to more rural areas, on the Shinkansen, would she be allowed?

If dogs are generally not allowed on trains, is there any kind of either mass transit or individual transit which accepts transporting dogs? I don't plan to own a car, so it's important for me that there be some way to get around with her if I need to.

To summarize, are dogs allowed on any sort of mass transit in/around Tokyo? And if not, what are the possible ways to transport me and my dog without owning my own vehicle?

Sorry, you cannot take a dog above 10kg on a train in Japan. Per JR East's rules, dogs and other animals can only be transported if they're placed in a fully enclosed crate less than 70cm in length and 10kg in combined weight, plus you need to pay 280yen per ride for the privilege:

有料のもの

●小犬、猫、鳩またはこれらに類する小動物（猛獣やへびの類を除く）で、

長さ70センチ以内で、タテ・ヨコ・高さの合計が90センチ程度のケースにいれたもの

ケースと動物を合わせた重さが10キロ以内のもの

https://www.jreast.co.jp/kippu/20.html

Rules may vary slightly between companies but the general gist will be the same for buses, trains, etc.

You should also be aware that importing a dog into Japan may require a quarantine period of up to 180 days, and that tiny apartments and long working hours and commutes are not very compatible with large dog ownership. Small "cute" dogs are popular but I've rarely seen large dogs outside rural areas.

Update: I did find one (1) taxi company in greater Tokyo that carries pets small or large: http://smile-animaltaxi.com/

It's not cheap though, with rates starting from 4000 yen for 5 km.

Yamato Unyo, one of the delivery companies, will apparently transport a crated dog from Narita Airport to almost anywhere: https://form.008008.jp/mitumori/PPET0100Action_doInit.action

They will transport medium size dogs up to 30kg and large dogs over 30kg, so you’re in the clear.

They’re pretty much your only option for larger size animals even though they are pricey. Public transportation options tend to restrict dogs to only small ones less than 10kg that can fit in their own bag. Rental cars don’t allow animals that aren’t crated and a one-way rental from Narita is going to be expensive, let alone not something I’d recommend a newby try (left-side driving, Tokyo traffic, jet lag, a barking dog, etc).

For general travel in Japan, everyone I know either checks their dog in at a dog hotel (of which there are plenty) or has their own car.

If you do go with Yamato, it looks like you need to make a reservation and get a quote, which makes sense as there’s likely a lot of prep work needed on the transportation company’s end.

Finally, your company may have a relocation specialist on staff or on contract. You may want to contact them as they as usually familiar with slightly odd requests from foreigners.