Jen, I hope Josephine will answer you soon and ease your mind with her expert comments. But I think generally you can have a fever from a sickness or virus and it would not effect your knees. I know how that kind of thing can worry you, though. I was really concerned not too long ago when I found a tick buried in my upper leg. Because of all the tick-bourne illnesses and the fact that they have their head stuck in your blood supply, I was wondering if maybe I shouldn't take an antibiotic to be sure my knee was protected. But the consensus from Josephine and my doctors was that it was not necessary. Although they didn't say it directly, I'm thinking that you would have to have a major infection - like staph - for there to be a potential for knee problems. But....since I'm no expert, hopefully Josephine will come to your rescue here very soon. In the meantime, I hope you feel better soon. Rest, drink fluids, aspirin or fever reducer, and the aches sould go away soon. I am assuming there is no redness or swelling out of the ordinary around your knees, right??