This study aims to explore the effects of argumentation with the concept map method during medical problem-based learning (PBL) on individual clinical reasoning. Individual clinical reasoning ability was assessed through problem-solving performance and arguments that students constructed during individual clinical reasoning processes. Toulmin's model of argument was utilized as a structure for arguments. The study also explored whether there would be any differences between the first-and second-year medical students. Ninety-five medical students participated in this study, and they took two PBL modules. During PBL, they were asked as a group to construct concept maps based on their argumentation about a case under discussion. Before and after each PBL, they were asked to write individual clinical problem-solving tests. One-way, within-subjects ANOVAs were conducted to examine the quality of arguments and clinical problem-solving performance in three individual tests. The results provided evidence that utilizing argumentation with the concept map method during PBL positively affects the development of clinical reasoning skills by individual students.