Acute and chronic prostatitis discussion. Arnon Krongrad, MD, moderator.
Well, without being a medical professional, it does not seem perhaps too unexpected that if you have some condition which your body's immune system is fighting then if you don't get sleep then maybe the immune system is not so strong and the condition gets worse. Some of my worst flare ups have been after a week of really bad sleep - seems to be a trigger for me.
Alternatively, lets consider the other scenario that there is no infection but just some unexplained prostate inflammation of some sort/nerve compression/something else, it could be that when you are very tired you don't have the same posture and so there is more compression of the sensitive parts.
Or it could be that when you are tired, you unconsciously sit down more, thus putting more pressure on the sensitive areas.
I've always found the end of the day much more uncomfortable than the start, even when I've avoided sitting. Could be for any of the above reasons.