Objective To explore how to perform problem-based learning (PBL) in early clinical education for junior medical students. Methods 30 medical undergraduates in grade one and grade two named PBL group received PBL during pre-internship in department of internal medicine. 40 medical undergraduates of their classmates named control group received regular pre-internship without PBL. Results Compared to the students in control group, the students in PBL group thought the contents of their learning were more specific, they could have more achieves as well as more chance of communication with each other during the pre-internship, and they had more interest in pre-internship and clinical activities. Most of them made great progress in self-learning, problem-solving and self-expression. All of them would like to continue PBL during pre-internship in the future. Conclusions Pre-internship with PBL is a good complement for traditional teaching. It can not only improve junior medical students' interests in clinical activities, but also raise their capacities such as serf-learning, practice and spirit of team work.