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This study aims to determine the differences and the effect of the Problem-Based Learning (PBL) model assisted by animated videos on junior high school students’ critical thinking skills in the solar system topic. A quantitative approach with a quasi-experimental nonequivalent control group pretest–posttest design was employed. The research subjects consisted of two seventh-grade classes at a public junior high school in Yogyakarta, selected using cluster random sampling. Research instruments included multiple-choice tests to measure critical thinking skills and observation sheets to evaluate the implementation fidelity of the learning model. Data were analyzed using the Independent Sample T-Test and effect size calculated through Cohen’s d. The results showed that the PBL model assisted by animated videos significantly improved students’ critical thinking skills, with the effect size categorized as moderate. The novelty of this study lies in the integration of animated video media within the PBL framework, which enhances contextual understanding and supports students in problem exploration related to astronomical phenomena. The findings imply that combining PBL with animated media can serve as an effective pedagogical strategy for strengthening higher-order thinking skills in science learning, and can be considered for wider implementation in junior high school settings.