This study investigates the integration of critical thinking activities into English Mediated Instruction (EMI) to cultivate higher-order learning skills among university students in Japan taking a foundational course on critical thinking skill development. Drawing on theoretical frameworks of critical thinking and educational philosophy, the research presents a praxis approach from conceptualizing activities to implementation. The study highlights scaffolding techniques as the pedagogical tools to actualize intended activities in practice. As part of the praxis process, students’ voices are included in the research from their reflective writing in journals. Through a qualitative analysis of student perspectives and reflections, the study evaluates the effectiveness of these activities in promoting critical thinking within an EMI context. Three specific activities are examined: analyzing Plato’s Allegory of the Cave; deliberating on ethical dilemmas in drone warfare; and engaging in collaborative presentations on various ethical issues. The findings highlight students’ enhanced self-awareness, ability to welcome multiple perspectives, recognition of the importance of ongoing learning, and development of practical critical thinking skills. By providing a comprehensive account of pedagogical design, implementation, and student outcomes, this research bridges the gap between theoretical frameworks and practical application, offering insights for educators to enrich students’ critical thinking abilities in diverse academic environments.