Background: Augmented reality (AR) is a widely used technology in science education today. Problem-based learning (PBL) is one of the teaching methods employed in science education for a long time. Studies where AR and PBL are used together are new and rare. PBL and AR technology are used together in the study because it is believed that integrating AR technology with PBL increases the effectiveness of PBL. Objectives: In the present study, the effect of PBL supported by AR on academic achievement, reflective thinking skills towards problem-solving, decision-making abilities, and the permanence levels of the 7th-grade students were researched. Methods: The embedded design from mixed methods was used in the study, which had two experimental groups and one control group. For the Experiment-1, Experiment-2, and Control Groups, respectively, PBL supported by AR, PBL alone, and the current teaching method were used. The sample consists of 92 students from the seventh grade. Results and Conclusions: In terms of academic achievement, reflective thinking skills towards problem-solving, and decision-making abilities, the Experiment-1 Group outperformed the Experiment-2 and Control Groups, and the Experiment-2 Group outperformed the Control Group. It has been discovered that PBL supported by AR is more effective than solely PBL and the currently used teaching method in terms of improving reflective thinking skills towards problem-solving and decision-making abilities, as well as the persistence of academic achievement in a science course.