Recently adopted kitten hiding and not eating.

Hello, I'm on mobile, so I apologize for the lack of formatting.

I recently adopted a bonded pair of kittens from my local shelter. They are 5 months (girl), and 4 months (boy) old. The girl has been awesome so far, she took to my apartment like she owned it almost immediately and has been very social. The boy however has done nothing but hide. I know it's only been like two days, but he has not been eating, and because of that, the other kitten keeps stealing his food.

I was wondering if it would be a good idea to keep him in a locked room for a few days until he starts eating and exploring more. I was thinking about my bathroom for this. I live in a one bedroom apartment, and I'm afraid if I use my bedroom, he won't come out while my girlfriend and I are sleeping (I work nights, and she works days, so we have kinda opposite schedules). Plus, he has a habit of squeezing into places and getting himself stuck. He recently squeezed under my dresser and meowed till I moved it, then ran off and hid in a litterbox for a few hours.

What do you all think I should do? I know the bathroom is kinda small, but I'm afraid if I leave him in the bedroom he won't come out if someone is in there, or our other cat will continue to eat his food. I'm also kinda worried about breaking their bond if I seperate them.

I would leave him in the bathroom, with a litter box, food and water. I think he's needing a smaller room to adjust to, before you expose him to the larger/general area. Or, you could put food and water with him where ever he's hiding - under the bed, in a closet (left half open). 

Sometimes cats take a while before they're comfortable in their new home. My cat took 2 weeks of hiding under the couch to feel comfortable. Hang in there, and don't rush the process. Let him come out when he's ready!!  

One of the cats will always be more dominent than the other. I still have to pull my male cat away to let the female eat properly.

Putting him in a smaller space may be a good idea, depending on how he reacts to it. I'd test it out first. I had a kitten who hated being locked up all alone. I only tried it once and he's still pretty sensitive about being in that room. Maybe you should just let him do his own thing. It's still pretty early. Im sure he'll adjust.

But if he gets into the habit of hiding after a couple weeks then I might consult the vet for further info.

Since you're in a one bedroom and your kitties have been there for a couple of days I don't think its worth to lock up the boy. You may want to feed them separately though and maybe leave them separated for about an hour after feed to make sure he eats.

Give him more time and he'll come out of his shell.

UPDATE: We tried shutting him in the bathroom for the night when I was at work.  My girlfriend said he started crying and scratching at the door, but stopped after about 20 minutes.  When I got off work in the morning, he had eaten some of his food and used the litterbox.  We decided it was probably not a good idea to shut him in there again.  When I was at work the following night, she started sending me pictures and videos of him roaming the apartment.  I think it's actually me he's afraid of.  I know he was fostered by two women, so I don't know if it's me personally, or just because I'm a male.  He will let me reach under the couch and pet him, he just won't come out around me.

Honestly just give it some time. He will adjust. It seems like he's just adjusting slowly