Problem-based learning (PBL) is defined as a student-centered pedagogy which can provide learners more opportunities for application of knowledge acquired from basic science to the working situations than traditional lecture-based learning (LBL) method. In China, PBL is increasingly popular among preventive medicine educators, and multiple studies have investigated the effectiveness of PBL pedagogy in preventive medicine education. A pooled analysis based on 15 studies was performed to obtain an overall estimate of the effectiveness of PBL on learning outcomes of preventive medicine. Overall, PBL was associated with a significant increase in students' theoretical examination scores (SMD = 0.62, 95% CI = 0.41-0.83) than LBL. For the attitude- and skill-based outcomes, the pooled PBL effects were also significant among learning attitude (OR = 3.62, 95% CI = 2.40-5.16), problem solved skill (OR = 4.80, 95% CI = 2.01-11.46), self-directed learning skill (OR = 5.81, 95% CI = 3.11-10.85), and collaborative skill (OR = 4.21, 95% CI = 0.96-18.45). Sensitivity analysis showed that the exclusion of a single study did not influence the estimation. Our results suggest that PBL of preventive medicine education in China appears to be more effective than LBL in improving knowledge, attitude and skills.