Objectives: This study aimed to assess the perception of PBL among Japanese medical students.Methods: Learning effects and challenges of PBL from the students' viewpoint were assessed with an exploratory se-quential mixed method. Focus group discussions followed by thematic analysis were conducted with 27 students and resi-dents. Then a questionnaire survey was carried out. A total of 119 out of 258 students (46.1%) responded. The results from 24 questions were analyzed with a residual analysis.Results: Thematic analysis extracted 14 themes from four discussion topics. The participants in focus group discussion regarded the PBL program as a better learning method than lectures. But some key phrases on the challenge of social in-teraction, including reluctance to actively discuss and collab-orate with unfamiliar peers, were found. The questionnaire survey revealed a significantly lower adjusted standardized residual (ASR) for the positive response in five of six ques-tions in the category of social interaction; improvement of communication skills (ASR =-3.303, n = 118, p < .001), en-hancement of responsibility at group discussions (ASR =-2.078, n = 119, p = .038), building social networking (ASR =-3.006, n = 119, p = .003), becoming to sympathize with patients (ASR =-2.449, n = 119, p = .014) and under-standing social aspects of clinical practice (ASR =-5.790, n = 119, p < .001). Conclusion: The Japanese medical students perceived PBL as an effective learning strategy. However, they had a prob-lem with social interactions.