Shortly before the school term is over, a peeping attempt goes wrong and results in middle school student Yuuichi Kanba reconnecting with his childhood friend Makio Fujiyama, a girl who stands taller than the rest of her classmates at 181 cm. After seeing her undress, feelings of affection begin to blossom within Kanba, despite Fujiyama being considered unattractive by both peers and passersby. Kanba asks her out on an impulse and—to his surprise—she says yes.

Through school events, fireworks festivals, and more, Kanba juggles gawking at his new girlfriend and keeping their relationship a secret. This is no easy task for the less-than-popular Kanba, as Fujiyama often draws the eyes of all around her.

Fuijyama-san wa Shishunki follows the pair as they stumble hand-in-hand through many lighthearted, comedic situations and gradually learn more about young love and each other.