Games have rapidly grown into the pinnacle of educational technology across many levels and subjects. Additionally, educational games are most potent when they complement game mechanics with a narrative, most practically done via quests. Yet, educational games still lack an efficient and general design method for quest systems. To address this research gap, we present a design method comprising a high-level conceptual model, a UML-based metamodel, and a quest modification algorithm. Based on state-of-the-art theories of human learning and game quests, the high-level model concisely describes the systemic constituents of a quest system split into subsystems for a storyworld, storytelling, assets, and UIs, which align with the cognitive, affective, and sensorimotor learning domains. Similarly, the UML-based metamodel adapts relevant metamodels and domain-specific modeling languages for educational media. Moreover, the algorithm allows easy modification of the resulting quest system, ensuring the system’s flexibility. We implemented the high-level model and metamodel in a case study of developing an educational role-playing game (RPG) with two separate yet overlapping questlines: one on software development process models and another on environmental education. The results of the RPG’s playtest by university students and the evaluation of its quest system by software engineers show how our design method can accommodate designing a quest-based educational narrative game with a flexible quest sequence for not just one but multiple learning purposes.