I really like Onsen Shinjuku Ryokan Yuen which is kind of a business hotel and ryokan hybrid.
I’ve spoken in detail here about why Shinjuku is probably my least favourite areas to stay with kids but if you really still want to be in this area, this is my number one choice for families in Shinjuku.
Rooms here are small, modern, clean. Has a public bath for guests to use. Tattoos are generally not allowed but if are small can be covered with a sticker (stickers can be purchased at the front desk.) Each room also has their own ensuite (so the public bath isn’t your only bathing option.)
I often recommend this hotel as one of the options that are like a traditional ryokan but with a modern twist (and without the normal ryokan price tag or the pressure to eat all of the traditional food.)
Every person who stays gets a yukata (like a light kimono robe that is to be used for getting to and from the public bath and can also be used as pyjamas) to be worn during their stay.
There is a coin laundry on site for guests to use and a convenience store just out the front of the hotel.
*A little note on coin laundries in hotels in Japan. The detergent is almost always built into the machine. If someone in your family has allergies to certain washing powders it is probably best to email in advance to find out what they use and what your options are. Oh.. and another note.. if the washer and dryer is built into one machine – the dryer setting really only works well for 1-2 items (big items like a pair of jeans and a long sleeved top, I mean) so don’t do what I do and just put in heaps of things to dry for longer – hoping that they will dry. It doesn’t work like that. Best to do little tiny drying sessions for the best drying results. It a lesson in patience but it will save you lots of coins in the long run
This hotel is also happy to help you forward your luggage. I have more information on forwarding luggage in Japan here.
There is a 24 hour front desk too which is so handy if kids were to get sick while you are in Japan.
Their suite and premium double rooms can accommodate up to 4 people. Otherwise the rooms are on the more affordable side so, if possible, you may want to look into booking two rooms here for a larger family. You can also reserve a room rate that includes breakfast (western or traditional Japanese breakfast.)
Onsen Shinjuku Ryokan Yuen also have an in-house teppanyaki and tempura restaurant. Budget here for lunch is around 2500 yen and more like 8000 yen per adult at dinner time. It’s a kind of upscale restaurant so if you take children they will need to be able to sit in their own seats and I’d also bring some colouring or something to keep them busy at the table (nothing noisy like an iPad.) Onsen Shinjuku Ryokan Yuen is 7 mins walk from exit 3 of Shinjuku-Gyoen Mae on the Marunouchi Line or 5 mins (approx 700 yen) from Shinjuku Station.
From here, you can walk to Marui Shinjuku Annex and try out my favourite brand of 100 yen store called Seria.
And if the kids need a restaurant and a change from Japanese food, I can recommend very family friendly “Cafe La Boheme Shinjuku Goen” just 12 mins walk away.
Shinjuku Gyoen gardens are also just 11 mins walk away from the hotel. See my Shinjuku with kids blog post for details.
See here for other things to do in Shinjuku with kids.