Onsen separation?

I'm planning a trip for next summer (I'm obsessed with planning things early) that'll be me and my boyfriend. The thing is, my boyfriend is female to male trans, and as much as he wants to experience an onsen, he isn't comfortable being forced to go with all-women thanks to his body. Are there ones that don't separate people by gender? Examples would be nice so I could add them to my planning materials.

Thanks very much :)

Another option would be staying at Japanese traditional inns that have "kashikiri buro" (all-to-yourself bath) or "kazoku buro" (family bath) that you can rent by the hour or something like that to yourself. It will be a family sized bath within the inn (it may be outdoors or it may be indoors, that depends on the specific place) that you reserve for just the two of you to use. Would that be more comfortable for the two of you?

Once you know the city/town you are going to, probably some of us here can help you look up some places with this kind of bath available.

A time reserved Kashikiri private onsen bath is for you if you don't want to pay high rate for a small bath in-room or attached to the room.
It depends on which onsen town you go but there are many and for a day use, too.

Oh, I didn't think of the private ones! That would definitely work much better for us.

We're spending most of our trip in Tokyo, just exploring different parts each day. Our main base (the apartment we're renting) is in the Nishi-Ogikubo area, but I guess we can go anywhere in the main Tokyo area.

I'd love to know a few to check out specifically, if you can :)

Sorry, there is no real onsen in Tokyo. Well known onsen towns near & around Tokyo are Kusatsu, Hakone, Kinugawa, etc.

The hot spring doesn't have to be right in Tokyo. I'll check out those other areas.

I can't recall where exactly, but I have have come across some reviews of unisex onsen, which are still real onsen (not the artificial ones with tap water and added minerals).

I would think that if you did a search for "unisex onsen" you should quickly find something to your liking.

As said, a private onsen, be it a little bit steeper in price, is also an option. Especially if you want to be a little bit more intimate with each other.

(btw, early planning is good ^_^)

See if you can pick one here. It is the list of all Kashikiri private time reserved and in-room private onsens in Japan.
http://www.kashikiri-onsen.com/

Thanks guys! I've decided we're going to do a night in Hakone. I found a place with the private in-room option that I like...can't remember the name of the place off the top of my head, but it looks great.