"Magical Sempai" centers around a high school club dedicated to magic, led by an enthusiastic but clumsy magician known only as Sempai. Despite her passion for performing magic tricks, Sempai consistently struggles with stage fright and a lack of coordination, leading to frequent mishaps during her performances. Her earnest efforts to improve and her determination to entertain often result in comedic situations, particularly when her tricks go awry.

The story unfolds through the perspective of an unnamed male student, referred to as Assistant-kun, who stumbles upon the Magic Club while searching for a place to belong. Initially skeptical of Sempai's abilities, he becomes her reluctant assistant, helping her prepare and execute her tricks. Over time, Assistant-kun develops a deeper understanding of Sempai's dedication and begins to support her more earnestly, despite the chaotic and often embarrassing outcomes of their performances.

The series is episodic, with each episode featuring Sempai attempting new magic tricks or facing challenges related to her performances. The humor arises from her persistent failures, exaggerated reactions, and the dynamic between her and Assistant-kun, who often finds himself caught in the crossfire of her antics. Supporting characters, such as the stoic and mysterious Maid-chan and the competitive Magician-senpai, add variety to the narrative, occasionally challenging Sempai or providing additional comedic moments.

Themes of perseverance, friendship, and the pursuit of one's passions are subtly woven into the story, as Sempai's unwavering commitment to magic inspires those around her, even in the face of constant setbacks. The series balances lighthearted comedy with moments of genuine warmth, showcasing the bond between Sempai and Assistant-kun as they navigate the ups and downs of their magical endeavors.