PurposeResearchers have previously utilized the project-based 6E learning model and the problem-based quantum learning model in various courses, such as the instructional principles and methods course and the character and values education course. These models were evaluated for their impact on students in different subjects, including developing skills, values, democracy perceptions, attitudes towards cooperative learning, metacognitive thinking skills and teacher self-efficacy perceptions. In 2023, Ökmen, Sahin and Kiliç reported positive outcomes, while Sahin and Kiliç reported similar findings in 2023a, 2023b and 2023c. There has been no investigation into how the models affect students' critical thinking and academic literacy. This study seeks to determine the impact of both models on these skills, gain more insight into their effectiveness and determine which is more beneficial. The results will guide the decision-making process for the character and values education course and other courses in the future. Specifically, this research aims to compare the effects of the project-based 6E learning model and problem-based quantum learning model on critical thinking and academic literacy.Design/methodology/approachThis research employed the Solomon four-group experimental design to assess the efficacy of the applications. Prior knowledge and experience of the participants were evaluated through pretests. However, it should be noted that pretests may impact posttest scores either positively or negatively. For instance, participants taking the test multiple times may become more interested or attentive to the subject matter. The Solomon four-group design was deemed appropriate to analyze the influence of pretesting. This design enables the investigation of the application effect, pretest effect and interactive effect of pretest and application (van Engelenburg, 1999).FindingsIt was concluded that the project-based 6E learning model was effective in developing critical thinking in students, but not significantly. It was concluded that the problem-based quantum learning model significantly improved students' critical thinking skills. It was concluded at the end of the study that the project-based 6E learning model notably enhanced students' academic literacy. It was concluded that the problem-based quantum learning model had a significant positive impact on students' academic literacy. According to research, it has been determined that the problem-based quantum learning model is superior in enhancing critical thinking abilities compared to the project-based 6E learning model. Nevertheless, there seems to be no detectable disparity in the academic literacy advancement of pupils between the problem-based quantum learning model and the project-based 6E learning model.Originality/valueThere has been no investigation into how the models affect students' critical thinking and academic literacy. This study seeks to determine the impact of both models on these skills, gain more insight into their effectiveness and determine which is more beneficial. The results will guide the decision-making process for the character and values education course and other courses in the future.