Understanding scientific phenomena requires comprehension and application of the underlying causal relationships that describe those phenomena (Carey 2002). The current study examined the roles of self-explanation and meta-level feedback for understanding causal relationships described in a causal diagram. In this study, 63 Korean high-school students were randomly assigned to one of three conditions: instructional explanation, self-explanation, and meta-level feedback. Results showed that self-explaining a causal diagram was as effective as studying instructional explanations. Furthermore, the effectiveness of self-explaining a causal diagram was enhanced by meta-level feedback that prompted students to reflect on their own explanations by comparing them with instructional explanations. We identified three main difficulties that high-school students experienced when explaining a causal diagram to themselves: one-sided explanation, erroneous explanation, and the lack of inference. Implications of the study were discussed in regard to the improvement of self-explanation and the design of causal diagrams in science education.