Right now I have been using English sites for trying to find a place to stay for a trip in Japan. But are there any Japanese sites that might do a better job at it?
Would they have a larger list of places that aren't on the english sites? Or maybe let me narrow down the area to near a certain station or something like that?

They have a larger list but its more expensive on Japanese sites I find.
Japanese hotels are charged by the night and per person instead of just for the room, but rooms can be purchased on English sites on a room based price I find.
My recommendation is to stick to english sites like Expedia.

If you are hell bent on it though, the one I use most often is Rakuten. Rakuten Travel

I've only used Japanese sites for finding a ryokan, and the way many sites restrict the search region as if you know all about obscure locations in the Gunma countryside is pretty annoying.

I agree with Vix's suggestion to stick to English sites. Booking.com and Agoda.com are another couple worth checking along with Expedia.

Wow, never heard of Agoda.com. This looks great. I can narrow it down to a smaller area than just "tokyo", and its showing me some amazing rates that I didn't find on other sites!

Zarxrax Wrote:Wow, never heard of Agoda.com. This looks great. I can narrow it down to a smaller area than just "tokyo", and its showing me some amazing rates that I didn't find on other sites!

You should be in commercials and... stuff.

It's not a typical hotel experience, but have you tried using airbnb.com? It lets you book apartments, roomshares, and houses by the night. I use it domestically all the time, but I've been looking for an upcoming trip to Japan and found a lot of sweet places with good pricing.

I've used http://www.hostels.com/ and can't say a bad word about them.

If you can manage using only Japanese I definitely recommend https://www.jalan.net/

I always use them and there are usually a ton of deals on there too! (I've gotten hotels as low as 1000 yen a night in Tokyo, like real hotels, not capsule ones). You can search for a lot of obscure places too.

I've used Rakuten, Jalan, and Rurubu a couple times each. They were more or less the same, but the last time I used them was years ago. So things might have changed a lot since then. In any case, if there was a difference, Rakuten was the worst offender of spamming my mailbox.

But my usual way is to search for holes/motels on google map (go to the location I'm planing to stay at and do a search with terms like ビジネスホテル and 旅館) and go straight to their official websites or simply call them, or look for deals online if I have the time and it's worth it.

It never occurred to me I could use foreign websites.