Phobias are actually very easy to deal with, AmyKay. It's just a desensitization process. I would call and get a referral for a child psychologist who specializes in phobias and desensitization, and get him started.
And before you do that buy him Harry and the Terrible Whatzit if you haven't already got it. About a boy who was afraid of the Whatzit in the basement, and didn't get over it until he confronted it.
This will get bigger, and bigger, and bigger until this fear has kind of "metasticized" into his whole brain - it already has. He already is refusing to go out.
The desensitization will involve him taking charge himself - first, talking about rain, looking at pictures of rain, listening to audio tapes of rain (something most people find soothing, actually) and culminate in standing outside during a rain shower.
And then he'll be much better. He'll be in control again.
Best wishes.
Has he been checked by a developmental specialist at all? My husband and two boys all have autism spectrum disorder issues. This sounds like something that would typically occur in an Asperger's syndrome child. They tend to be well behaved, very smart, kind of loners, and have certain things that just set them off. My husband and four year old son are both Aspie's. I would have him evaluated by a developmental specialist. My husband didn't find out that what he had was Asperger's until he was in his thrities. He really wishes he had known earlier because he could have made better choices with college and career stuff. Keep me posted on what you find out.