3 months + fever

Courtney
My nearly 3 month old is not feeling well. It's 2:30 am now and since 12 pm she has been cranky consistently. She is eating well, minimal spit up. I'd say she is even eating more than normal (breastfed but I did give her a 4 oz bottle of breast milk and then she nursed really well an hour later).
Since around appx 7 pm she has been running a small fever about 99.5. Every time I try and burp her, she starts crying (like a whiny cry and eventually will start screaming like she is hurting or something). And really every time I move the position of her body she cries. 
I feel like she probably has an upset stomach, but with her eating so well I'm not sure. Any thoughts or should I give doc a call?