Rory complains that her brain “pinged” or “dinked” while she was studying. It sounds like tinnitus, a fairly common condition where you hear phantom noises such as clicking, hissing, or roaring – these often seem to emanate from inside your head.
It can be brought on by stress, which fits with Rory studying hard to the point her head hurts. She never complains of it again, suggesting that the condition spontaneously resolved, which isn’t uncommon with tinnitus.
The Annotated Gilmore Girls 