Variation theory, which is a theory of learning developed by Marton and others, has quickly become popular in education research. Our purpose of this paper is to articulate the application of variation theory in the form of a number of concrete design principles that offer prescriptive and practical guidelines for improving the designs of educational software programs. To achieve this, we analyzed a wide range of educational software programs produced over the years in our previous projects for learning Chinese characters. From this analysis, we identified four design principles, namely, (i) not aiming to test but to bring about learning, (ii) focusing on a specific object of learning, (iii) allowing learners to explore variation to be learned, and (iv) keeping all other aspects invariant. These design principles are specialized for designing how learners interact with educational software programs, which is the major practical contribution of this paper.