"My Friend's Little Sister Has It In for Me!" centers on Akiteru Kusanagi, a high school student and aspiring light novel author who collaborates with his childhood friend Mashiro Shiromaru under the pen name "Aki." Together, they create a successful light novel series, but Akiteru hides his identity to avoid complications. Mashiro, a talented artist, is unaware of Akiteru's feelings for her, and their professional relationship remains strictly platonic.

The story takes a turn when Mashiro's younger sister, Iroha Shiromaru, discovers Akiteru's secret. Iroha, a popular and mischievous girl, decides to use this knowledge to her advantage, often teasing and manipulating Akiteru to get what she wants. Despite her playful antagonism, Iroha harbors her own feelings for Akiteru, creating a complex dynamic between the three characters.

As the narrative progresses, Akiteru navigates the challenges of balancing his writing career, his unspoken feelings for Mashiro, and Iroha's persistent interference. The series explores themes of unrequited love, sibling rivalry, and the struggles of creative collaboration. Supporting characters, such as Otoha Shiromaru, Iroha's twin sister, and other classmates, add depth to the story, often contributing to the comedic and dramatic moments that drive the plot forward.

The manga blends elements of romantic comedy and slice-of-life, with a focus on the interactions and emotional growth of its characters. The interplay between Akiteru, Mashiro, and Iroha forms the core of the story, with their relationships evolving as they confront misunderstandings, personal insecurities, and the pressures of their creative endeavors. The series maintains a lighthearted tone while delving into the complexities of young love and ambition.