Objectives The purpose of this study is to analyze the learning effects of problem-based learning(PBL) implemented in universities in Korea and to provide implications for the instructional design of PBL in higher education. Methods Researchers collected manuscripts published in academic journals and dissertations related to PBL conducted in Korea from 2010 to September 2022, and finally selected 116 studies following the PICOS approach. We conducted a meta-analysis to analyze the overall effects, the effect sizes for cognitive and affective variables, and the effects of moderating variables using CMA software. Results As a result of analyzing 392 effect sizes from the 116 research results, the overall effect size of PBL was 0.737, indicating an intermediate effect size. The effect sizes for cognitive and affective variables were 0.582 and 0.837 respectively, which indicates affective variables showed significantly higher effect size than cognitive variables. Moderating variables were academic domains, curriculum, learning environment, and program duration. Among the moderating effect of subgroups, the effect size of the academic domains was significantly larger in the order of humanities, social sciences, arts and physical education, natural sciences, and engineering. Regarding the curriculum variable, the effect size was significantly larger in the order of the teaching professional subjects curriculum, the major curriculum, and the liberal arts curriculum. Conclusions Based on the results, it was suggested that further research on the design and delivery of PBL in various learning environments is needed. The results of this study are expected to be used as a basis for effective PBL design in higher education.