"Josō Danshi wa Skirt o Nugitai!" centers on the life of Kōichi Mizuhara, a high school student who enjoys cross-dressing as a hobby. Despite his masculine appearance and demeanor, Kōichi finds comfort and self-expression in wearing skirts and feminine clothing. The story explores his daily life as he navigates the challenges of balancing his secret hobby with societal expectations and personal relationships.

Kōichi’s best friend, Tōma Sakai, is aware of his cross-dressing and supports him, often helping Kōichi shop for clothes or offering advice. Their friendship serves as a cornerstone of the narrative, highlighting themes of acceptance and understanding. Kōichi’s interactions with other classmates, including his crush, Yūka, further complicate his efforts to keep his hobby private while staying true to himself.

The plot delves into Kōichi’s internal struggles with self-acceptance and the fear of judgment from others. It also examines the reactions of those around him when his secret is eventually revealed, showcasing a range of responses from curiosity to prejudice. The series balances lighthearted moments, such as Kōichi’s enthusiasm for fashion and his humorous attempts to hide his hobby, with more serious reflections on identity and societal norms.

Throughout the story, Kōichi’s journey is marked by growth as he learns to embrace his individuality and confront the challenges of being different in a conformist environment. The narrative emphasizes the importance of self-expression and the value of supportive relationships, offering a nuanced portrayal of a character navigating a non-traditional path in a traditional setting.