Here are some options, depending on what you mean:
If you mean the black center of the eye:
* Iris (while technically the colored part, the pupil is the opening within the iris)
* Pupillary aperture (more technical)
If you mean a student:
* Learner
* Scholar
* Student (this is just the most common synonym)
* Disciple (implies a more devoted following)
If you mean the "pupil" of someone's eye:
* Ward (implies someone under your care)
* Protégé (implies someone you're mentoring)
It's important to consider the specific context to choose the most appropriate word.