Are you planning to regulate the voltage down to 12V or something lower? Case fans are specced for 12V, they're not designed to take a higher voltage/current than what that would deliver.
It should work fine as fans are low current really, however USB does have protocols in place to control current. Theoretically it will limit current unless a device identifies itself as accepting fast charging etc. Not all motherboard manufacturers comply fully with this special though.
I'm running a 12V fan off 5V USB on a 24/7 HTPC. Does it need to be external, or would it be easier to take 12V from inside the PC somewhere?