Why does my prostate ache?

Are you sure? I mean, how do you know it's your prostate? That walnut sized organ is buried deep inside your rectum. With that said, prostatitis can present as tenderness in the perineum in the area between the scrotum and the anus, making it difficult to sit for long periods of time. But it commonly presents w/painful frequent urgent urination, similar to bladder infection. Go see your family doctor.