Consider that pronation of the wrist - when your palms are facing your desk - isn't a natural position. You're kind of making an "X" with your ulna and radius bones in your forearms. Not natural. It's not really natural to type, and its not natural to remain in a single position for an extended period of time. An ergonomic tower mouse, like an Evoluent vertical mouse, can be really helpful if he uses the mouse a lot because you pronate the wrist when you mouse.
Proper ergonomics can definitely help - a wrist rest, making sure the keyboard is at an appropriate height so the elbows are close to a 90-degree angle, maybe a keyboard tray, etc.
There are plenty of guides on workstation ergonomics online. Physical therapy may help, so he should definitely seek assistance from a primary care physician if it gets too bad. He might be able to get assistance from your employer's worker's comp if it gets serious. But once these type of issues get serious, they often dog people for a long time and frequently require surgery or multiple surgeries.
I do ergonomic evaluations for people at work - we have thousands of employees here - and proper positioning helps people a lot. He should mix up his tasks, too. If he has filing to do, he should break up his time on the keyboard and do it in the middle of the day, or sporadically throughout the day rather than saving it until the end of the day - that type of thing.