It could be a bunch of different things ... really hard to say. When I am fighting something off, this is how I start off being sick - I get headaches followed by fever. So to me, that sounds like he's fighting off an infection - like sinus or something. If it were ear, he'd likely be complaining about his ear, or throat - his throat. If his eyes are red - I'm guessing sinus, or from allergies which might lead to infection. Hard to say though. Keep an eye on him.
For me, the big thing is if they are not themselves. If they are listless or dehydrated. By listless I mean kind of non responsive - beyond lethargic from being sick.
Quick call to your doctor's office might help ease your concerns.
There are certain signs to look for if it's something serious. You could Google it - as in the case of meningitis, etc.
good luck hope he feels better soon