When participating in problem-based learning (PBL), it is important for medical students to generate claims and provide justifications for their claims in small group discussions. This study aimed to investigate the effect of argumentation instruction on medical student learning experiences with PBL. A total of one hundred first-year preclinical students from Inje University College of Medicine, who had attended argumentation instruction, participated in this study. All of the participants completed a 5-point Likert scale questionnaire regarding their learning experiences with PBL, before and after the argumentation instruction. The questionnaire comprised 22 items with eight subcategories: argumentation activity, reflection, integration of basic and clinical science, identification of lack of knowledge, logical thinking, self-directed study, communication, and attitude toward discussion. The collected data were analyzed through a paired-sample t-test. The results of this study found that the argumentation instruction promoted the preclinical students' experiences with argumentation activities, reflection, an integration of basic and clinical science, the identification of their lack of knowledge, logical thinking, and self-directed study, and it increased positive attitudes toward group discussion. The findings suggest argumentation instruction can enhance medical student group discussions and help students achieve the objectives of PBL, including acquisition of basic and clinical science knowledge and development of clinical reasoning and self-directed learning abilities, which can highlight the meaningful learning experiences students have with PBL.