Just before the semester ends, a failed peeping incident leads middle school student Yuuichi Kanba to reconnect with his childhood friend Makio Fujiyama, a girl who towers over her classmates at 181 cm. After catching a glimpse of her undressed, Kanba starts developing romantic feelings for Fujiyama, even though she is seen as unattractive by both peers and strangers. On a whim, he asks her out—and to his amazement, she agrees.
As they navigate school events, fireworks festivals, and other activities, Kanba struggles with sneaking glances at his new girlfriend while keeping their relationship under wraps. This proves challenging for the unpopular Kanba, since Fujiyama frequently draws the attention of everyone around her.
Fujiyama-san wa Shishunki follows the pair as they fumble hand in hand through a series of lighthearted, comedic situations, gradually discovering more about young love and each other.