Fever during urinary tract infection?

I went to the doctor and got prescribed Septra for a UTI. I started the medicine today and this morning I had a fever. I took tylenol and the fever went down for a little while, but now its getting late (when fevers usually get bad for me) and the fever is coming back. I just took more tylenol to get the fever down again. Is it bad to keep taking tylenol for a fever to keep it down? I have a 3 day prescription for Septra, should I wait for it to take its course, and keep taking tylenol to keep the fever down? What should I do?