The development of technology has driven a transformation in education, particularly in mastering 21st-century skills. However, students' learning motivation and critical thinking skills remain relatively low, largely due to the persistent use of teacher-centered conventional learning and the suboptimal integration of technology in the learning process. This study aims to determine the effect of the Problem-Based Flipped Learning (PBFL) model on students’ learning motivation and critical thinking skills in science, both simultaneously and partially. A quasi-experimental method was employed using a pretest–posttest nonequivalent control group design. The sample consisted of 80 students selected through group random sampling from a population of 404 seventh-grade students at SMP Santo Yoseph Denpasar.The data were collected using a learning motivation questionnaire and an essay-based critical thinking skills test, both of which were previously tested for validity and reliability. The data were then analyzed using Multivariate Analysis of Covariance (MANCOVA).The results revealed that the significance value was less than 0.05, indicating a significant difference between the PBFL model and the conventional learning model. The PBFL model demonstrated a substantial simultaneous effect on learning motivation and critical thinking skills (p = 0.001; ηp² = 0.355), and partially improved learning motivation (p = 0.001; ηp² = 0.349) and critical thinking skills (p = 0.001; ηp² = 0.145). In conclusion, the PBFL model is effective in improving students’ learning motivation and critical thinking skills in junior high school science education.
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