Purpose: The purpose of this study was to explain the challenges of using cooperative learning approach in higher education.Method: This research is a longitudinal study that has been conducted for two years on the experiences of an academic lecturer. The data of this research were gathered through reflection on the action and lecturer's autobiography and discussions with students who attended in the classroom, in three periods, before, during and after action, and were analyzed by coding and categorization. Data analysis revealed five main challenges in the areas of balance between content and method, academic space controversies, difficulty in learning assessment, increasing lecturer's duties, and lack of support and student’s role.Findings: The results of this study can clarify that if university lecturers want to use cooperative learning method in their teaching, they should prepare themselves to meet the challenges. Also, the results of the research show that if higher education policy makers and planners want to develop a cooperative approach in higher education, which problems they should support in practical ways.