First, you need to calm down about it yourself. Children cue off their parents' reactions. If you're freaked out, he will be too. The mildest disease is 100 times worse than a shot.
Second, don't lie about what it will be like, or else every time you go to a doctor he will expect the worst. Tell him the facts without either sensationalizing or minimizing. If he's the kind of person that gets scared easily, put off telling him until you're on the way to the doctor. Anticipation makes it worse.
Third, give him something else to concentrate on. Say something like, "It hurts, but it will hurt more if you wiggle too much. Look at me and try to stay as still as you can and relax your arm."
Lastly, some kids are going to have a hard time no matter what you do, so just get it over with as quickly as possible and remain calm yourself. My daughters cry during the event, but stop pretty much immediately after they're sure it's done. My son starts flipping out, screaming, and thrashing as soon as the needle comes out, and he stops listening to us, so about all we can do is hold him down so the needle won't break off inside him. He doesn't calm down until we're in the car, and he complains about the shot all day. We prepare all our kids in the same way. Sometimes it's just plain out of your hands.