Can Bactrim 100mg x 2 a day for 5 days cure a kidney infection? Yesterday when I went to my doctor for a UTI my back/flanks didnt hurt at all, today when I woke up and went to get my bactrim filled that he prescribed my flanks hurt. I think over night the bacteria may have traveled up to my kidneys. I read that bactirm isnt a preferred treatment for kidney infection only UTI, but the pharmacist said she thinks it would he ok for a kidney infection if it was early. Should I take the course of Bactrim and see what happens?