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Critical thinking is one of the skills that must be possessed in the 21st century. These skills can be improved by using the right media in learning. This study aims to examine the effectiveness of Flip PDF Professionals electronic module (e-module) lipid metabolism in problem-based learning to improve students critical thinking skills. E-module to be used has been previously made by the researcher and published. The research method used is T-test with research instruments test critical thinking skills in the form of pre-test and post-test. Tests are made based on the achievement of subject learning and critical thinking indicators that have been tested for content validation by lecturers. The subjects in this study were third-level students in Chemistry Education, Faculty of Mathematics and Natural Sciences, Universitas Negeri Jakarta. The results of the study show that the use of e-modules in problem based learning is effective for improving students critical thinking skills.