Critical thinking is highly valued as an integral skill for promoting students’ development, and problem-based learning (PBL) is widely used as an essential method to facilitate the development of critical thinking. However, since individual studies cannot determine the precise overall effect size of PBL on the development of critical thinking, it is difficult to systematically analyze the various influencing factors that hinder PBL from achieving sufficient effectiveness. Therefore, this study adopts a meta-analysis method to examine PBL in depth, aiming to clarify the crucial methods and elements of applying PBL to enhance critical thinking and address the shortcomings of existing studies. This study investigates two primary questions: first, the efficacy of PBL in enhancing critical thinking skills in comparison to traditional pedagogical approaches, and second, the influence of moderating variables on the effectiveness of PBL. To address these questions, a total of 25 studies were selected for meta-analysis. The findings revealed an overall effect size of 1.081 under the random-effects model, with a confidence interval of [0.874, 1.288] and p < .05, indicating that PBL significantly outperforms traditional methods. The analysis demonstrated that the effectiveness of PBL is not significantly influenced by learning stage, sample size, or measurement tools, thereby broadening the applicability of PBL and challenging preconceived limitations associated with its implementation. However, the results also indicated that PBL effectiveness is moderated by teaching methods and subject types, which offers critical insights for educators seeking to adapt their instructional strategies when employing PBL.