A fever generally is more of a sign of an illness - virus or infection - than pregnancy. Pregnancy does increase your temp, but not by very much. Illness can also cause your period to be late.
Also, at your young age, your cycle can get weird every now and then.
I recommend you go to see a doctor. And get some rest - you probably have the flu or something.
Side note: It's great you are using a condom... keep it up. But, to be on the safe side, you might also want to consider getting on birth control. Condoms do break sometimes and it's good to have that safety net to prevent pregnancy.