Q:

Story about a student that does not learn like other students

This student doesn't learn by rote and is singled out as an individual thinker that can innovate.
He was fearful that he would not pass his exams about repairing space craft but in the end he proves to be much better than the other students.

A:

Sounds like a garbled memory of "Profession" (1957) by Isaac Asimov, where the student in question cannot learn a profession direct from the machines, but must learn the old-fashioned way. He eventually learns he has been chosen to create the programs for the teaching machines.
A full version is available to read online here

