The question is too broad for specific advice. Since tracking implies movement it is hard to be specific without seeing it- post a clip and you will get better help.
In principle 3d tracking of an eye pupil can be done. You will need a 3d tracker for that. SynthEyes should do the job. Voodoo also... but there may be other options.
It would be beneficial to tell us what you are trying to accomplish as well.
Thank u for responding. I am shooting a movie in which several characters will have an eye replacement. Now if they just stare straight ahead I can easily use Andrew kramers effect. But if they turn there head from left to right they effect doesnt work as well. My question is how would I fix this problem. Now I know I would probably need a 3d tracker but Im on a tight budget. I know voodoo is free for windows users but I cant find something like that for mac.
You may not necessarily need a 3d tracker. You may be able to use Mocha (free with AE) and track the location of the eye. Then you can use the track data to cut a mask for the shape of the eye- some manual adjustment will be necessary- and to comp behind a layer on which you apply CC Sphere (for the eye replacement). You will then have to animate the rotation of the sphere to match the rotation of the head.