In the current conditions of updating the content of school education, the development of students’ research skills becomes especially relevant as a basis for forming critical thinking, cognitive autonomy, and independent learning. The article examines theoretical and practical aspects of developing research skills of ninth-grade students in an intellectual learning environment. The purpose of the study is to substantiate and pilot a model for developing students’ research skills based on the research method and tutor guidance. The methodological basis of the study included an analysis of scientific and pedagogical sources, a SWOT analysis of the implementation of a research project, pedagogical observation of the process of organizing research activities, student surveys, and analysis of the products of their project work. The study involved 113 ninth-grade students of the Nazarbayev Intellectual School of Physics and Mathematics in Taldykorgan, which made it possible to determine the level of their academic activity and the degree of involvement in project-based research activities. The results of the study indicate a positive dynamic in the development of research skills, critical thinking, and cognitive autonomy of students. Within the framework of the study, a model for developing students’ research skills and a methodological guide for creating a student-authored educational research project were developed and piloted. The practical significance of the study lies in the possibility of using the proposed model and the developed guide for organizing students’ research activities in the educational practice of general education institutions and schools with in-depth study of subjects under tutor guidance.