Can kidney stones that are still in the kidney cause pain?

I have had flank pain for over a month now. CT scan just shows a kidney stone in the kidney and the Dr.says it shouldn't cause pain. But it is not my imagination, it hurts in the area of my kidney. The Dr. just wants to give me antibiotics even though the urinalysis was clean. Just wondering if anyone has heard of this causing pain or is the Dr. right?