In Store -> Shipping -> Fedex Realtime Rates you could set up the realtime shipping rates via Fedex web service.
Please go to Fedex website http://www.fedex.com/us/developer/ to sign up an account and get User Key, Security Code, Account Number and Meter Number. After you get all these, you can fill out the form for Fedex Realtime Rates. Be sure to check the check box "Send to Production Server".