Researchers have suggested that case library learning is an effective instructional method that promotes argumentation skills for ill-structured problem-solving. However, little research has examined scaffolding strategies to implement effective case library learning. The aim of this research was to examine the effects of indexing prompts as scaffolds on argumentation skills during problem-solving in case library learning. A quasi-experimental design was employed for the research. A total of 111 first-year students in a university across three sections in a career development course participated in the experiment. Participants were provided with three different indexing prompts: explanation-based indexing prompts (focused on self-explaining anomalies of individual cases), difference-based indexing prompts (focused on self-explaining similarities and differences between cases), and no prompts (allowing spontaneous self-explanations when studying cases). Learners’ argumentation essays comprising initial arguments, counterarguments, and rebuttals were collected. The results found that learners who were prompted to generate mental indices outperformed the learners in the control group when constructing argumentation. More specifically, explanation-based indices were beneficial in making counterarguments and rebuttals, and difference-based indices were helpful when making rebuttals. These findings suggest that indexing cases based on both exploration of the anomalies of each case and comparisons between cases improves argumentation by facilitating case retention, retrieval, and reuse.