That would generally indicate too low a saddle. I've had pain right above the kneecap, and that was muscular tightness.
I would recommend trying to raise your seat in small increments (1mm) and give it a ride or two to test how it feels. A change of 15mm is huge, and makes a big difference in how your body feels. I was doing a 100k, and about 40 ish miles in, my seat post collar failed, and then the bolt seized trying to fix it. My saddle was at least 2cm below where it should be. Inside 2 miles, my knees were painful, and my hip flexors were in agony. It makes a difference that much, at least to me.
However, wait until your knee has rested up and doesn't hurt before you start testing raising the saddle. If it still hurts now, then try some ice and/or aleve to help reduce the irritation and inflammation.