Limited information exists on the effects of an oral and maxillofacial surgery integrated problem-based learning (PBL) course for dental undergraduates and the performance of these students after graduation. Therefore, we designed a PBL-implemented course with integrated dental alveolar surgery to evaluate its effects on the preparedness of graduates for clinical practice, their lifelong learning habits and their ability to collaborate, compared with the results of traditional courses. A randomised controlled trial was performed with 90 undergraduate students. The undergraduates were asked to perform a theoretical examination and to complete a clinical case analysis at the end of the course. Three years later, a follow-up survey was administered via a telephone interview and a questionnaire that measured self-perceived and supervisor-rated preparedness for clinical practice related to professional knowledge of dental alveolar surgery, lifelong learning habits, attitude and collaboration ability. All results were analysed using one-way analysis of variance (ANOVA) and a t-test. At the 3-year post-graduation time point, both PBL graduates and their supervisors rated their preparation for clinical practice as higher than those who received traditional lecture-based courses. In addition, the respondents in the PBL group believed that they were more likely than their counterparts in the traditional group to consult with professionals and other health-care staff members. No significant between-group differences were observed in the graduates' habits or lifelong learning attitudes. The PBL mode of teaching integrated dental alveolar surgery may improve preparedness for clinical practice and help undergraduates to develop the desire to collaborate.