Why does my baby cry every time she pees?

Urinary infection. If your child cries every time he or she pees, it could be a sign of an urinary tract infection. The rate of urinary tract infections in babies is higher in girls and in uncircumcised boys. Other signs include irritability, fever, difficulty feeding, and vomiting. Your doctor can check your baby's urine to diagnose a urinary tract infection.
Possible infection. Pain with urinating can be a sign of urinary tract infection or irritation of the urethra or vagina (in girls). Check the external genital areas for redness or irritation. Keep the area clean and coated with a barrier ointment. Have the baby checked by the pediatrician to make sure there is not a serious infection.