Reaching a period of life where they are neither a child nor an adult, 12-year-old Hanabi Ayase and Aoi Yui meet with life-changing events. Due to the mischievous demeanor of her male classmates, Ayase does not think highly of the opposite sex. However, her perspective begins to change after she is paired with the kind-hearted Takao Yuuto for a class assignment and unexpectedly shared their first kisses with each other on the school rooftop.

With her best friend discovering love, Aoi yearns to seek her own. She finds herself falling in love with the rash Kazuma Hiyama after protecting her from a rejected suitor who had talked behind her back.

12-sai.: Chicchana Mune no Tokimeki follows the four in this phase of adolescence. As they grow up alongside each other, this sweet romance depicts the innocence and excitement of first love.