K.B.
If you haven't already asked her where it hurts. With my daughter, who is 3 years old, we have a hard time getting her to discribe what hurts so we ask her to point where it hurts.
She might have an ear infection, which for some children are only noticable when they lay down for nap/bedtime and feel uncomfortable.
As Rachel said it could be growing pains but that only last for 2-3 weeks.
Hopefully it can be figured out. Feel free to call the doctor and maybe go in to see if further answers can be gotten.