"Shimajirō to Sora Tobu Fune" centers on Shimajirō, a cheerful and curious young tiger, and his friends as they embark on an adventurous journey aboard a magical flying ship. The story begins when Shimajirō and his companions—Mimii the rabbit, Ruru the bear, and Torippii the bird—discover a mysterious ship capable of soaring through the skies. This ship, powered by the dreams and imagination of children, becomes the vessel for their exploration of fantastical worlds and encounters with unique characters.

As the group travels, they face various challenges and puzzles that require teamwork, creativity, and problem-solving to overcome. Each destination introduces new themes, such as friendship, courage, and the importance of helping others. The narrative emphasizes the value of curiosity and learning, as Shimajirō and his friends often find themselves in situations where they must understand and adapt to unfamiliar environments.

The main characters are designed to appeal to younger audiences, with Shimajirō serving as the optimistic and inquisitive leader. Mimii provides a nurturing and supportive presence, while Ruru adds a playful and energetic dynamic. Torippii, with his ability to fly, often assists in navigating and exploring new areas. Together, they form a cohesive group that models positive social interactions and collaborative problem-solving.

The series is structured around episodic adventures, with each episode presenting a self-contained story that contributes to the overarching theme of exploration and discovery. The flying ship serves as a central motif, symbolizing the boundless possibilities of imagination and the joy of learning through experience. The narrative is straightforward and accessible, making it suitable for its target audience of young children while maintaining a sense of wonder and excitement throughout.