The development of students’ scientific thinking has become a key priority in higher education, particularly within courses focused on research methodology. Scientific thinking enables students to analyze problems systematically, formulate research questions, and apply appropriate methodological approaches. This article examines the pedagogical foundations for developing students’ scientific thinking in the course “Research Methodology.” The study analyzes theoretical perspectives on scientific thinking, pedagogical principles, and instructional strategies that support students’ research-oriented cognitive development. Based on a pedagogical analysis of contemporary educational practices, the article identifies effective teaching methods that enhance analytical reasoning, methodological awareness, and research creativity. The findings highlight the importance of integrative, student-centered, and reflective teaching approaches in fostering scientific thinking skills among university students.