What can we do to make a new student who speaks no English comfortable at our elementary school?

Is he having any ESL instruction? He needs to be working with an ESL specialist, too. If your school doesn't have one, contact the district, if not, your county/region ISD. This person can help you a lot with modifying your curriculum, helping with cultural differences, etc.

If he won't come into the room, is it possible that he can come in before school, before the other kids get there?

I agree with the buddy concept, too.

Or what if you could teach all the students to say "Welcome" or "Good Morning," or "Nice to Meet You," and hand him a little card with their name on it, or a happy picture. Or sing him a song? It's hard to know, without knowing the rest of your kids... do your kids know what's going on? Have you had a talk with them about being new, in a strange place, or what it's like to only hear a different language? Maybe exposing them to a little bit to culture shock might help them empathize.

The longer he stays out, the more freaked out he is going to become. Maybe your students could wear name tags, and help him say their names.

He is going through culture shock. Linguistic, cultural, mental overload. He's disoriented, and confused. If you have time, learn some simple phrases in Japanese. Hello, we are your friends, it's okay, do you need anything? etc. Also, a picture book (like "Point It" - link below), might help him show you what he wants/needs. Otherwise, some simple pictures with the word in Japanese and English underneath (play, bathroom, lunch, pencil, etc), will help him communicate with you, and vice versa. He can point to the pictures, and maybe the two of you can say the words in Japanese and English. Or you can point to the picture ("Art"), before you switch gears, so he knows what's going on. Lots of praise, smiling, and squatting down at his height might ease his mind a bit.

Picture book:

http://www.amazon.com/Point-Travellers-Language-Di...

(although, any sort of picture dictionary would be fine)

Info on Japanese elementary schools (notice the focus on small groups, cooperation. Our traditional system of whole-group instruction and competition might be freaking him out a bit, too).

http://en.wikipedia.org/wiki/Elementary_school_in_...

Japanese phrases. It would be totally okay for you to carry these around with you. These are just a few a googled:

http://genkienglish.net/genkijapan/japanese.htm

http://www.cnfj.navy.mil/phrases.html

http://www2.tokai.or.jp/yuki/japanese_words_and_ph...

http://www.japaneselifestyle.com.au/japanese_langu...

I worked in our school for a while and we had a similar situation. Our little girl was from China and she also didn't speak any English. What the teacher did was keep on with her daily lessons and not put any pressure on the child. This child would not eat, drink, or talk. Everything was different. The parents would not come in either. Slowly she began to pick up on the language, "No" just like babies is easy to learn and understand, I think that was her first word. The teacher assigned a student to the child, and she went everywhere with the student, lunch line, bathroom, learning the ways of America. By the end of the school year this little girl was speaking like a pro and was eating the food.

Please bear patience with the little boy, not only is he learning a new language, he is learning new food, new faces, he is only in third grade, he will pick it up and quickly. People from other countries handle things so different from us Americans, but in the end we are all equal. Let him follow a more learned student around for a month or so, he will learn the ropes. If you get stressed, it will make him stressed, go slowly, he is observing everything. Give it time.

At the start of the day you could pick a different student each day to teach them 3 new English words and then he can teach the class 3 new Japanese words. Possible only going to school for half days at beginning as well might not overwhelm him as much.

I love A M 's advice. Try not to show him you are upset by his behavior, not that I think you would be mean to him. It's just that because of the language barrier he will only have your face to comfort him. I love the idea of having one of your more patient kids help him out for a while. I would not switch up the children helping him at least not for a month or two, so that he has someone he really feels comfortable to be around. Please be vigilant that he does not get harassed in school, as this could set him back.