This study aims to analyze the effect of e-learning based on the problem-based learning (PBL) model on students' creative thinking skills during the COVID-19 pandemic. The research was conducted using quasi-experimental design and pretest post-test control group design, which was conducted at As-Shofa Islamic Senior High School, Pekanbaru, Indonesia class XII Science. The research used random sampling techniques. The parameter of this research was the skill to think creatively with four indicators, namely fluency, flexibility, originality, and elaboration. Data were gathered through the use of a creative thinking test in the form of a multiple-choice consisting of 20 items. The data of Min, Nmax, Nmin, Sd, and the effectiveness of creative thinking were calculated with the interpretation of the N-gain index (g). The results showed that the post-test average score of students' creative thinking skills in the experimental class using the PBL model through e-learning was higher than the control class without the PBL model, and the N-gain of the experimental class was higher than the control class. In conclusion, the PBL learning model through e-learning during COVID-19 pandemic affects students' creative thinking skills and was more effective, especially the original thinking and elaborate thinking skills when compared to learning without the PBL model.