As you can see, there are many reasons for a headache! Allergies are always a possiblility as well if the headache seems to coordinate with weather change, certain foods, after you clean the house, windows, tabletop, or as someone mentioned.....the heat trying out your house. You could try a humidifier for that. If it doesn't resolve quickly visiting the pediatrician is a good idea. The mom that had a child with strept throat.......some kids don't even a sore throat. Maybe just a headache and/or stomach ache.
Be sure your 3 year old knows what "headache" means. Try to get her to be more descriptive. She could be talking about her throat!