If your server is working very hard (Initial Bitcoin Download?) it may be running hot - causing the fan to run at high speed to keep the temperature in check.
If it is just a loud fan there may not be anything to do. If it sounds like the fan might actually be broken you should consider repairing / replacing the fan - hopefully under warranty.
Is this a DIY build? or did you purchase the server from Start9?
NOTE: If you are using a Server One we have instructions to turn off performance mode - that can reduce fan noise.- check out this thread: