Cooperative learning (CL) is a teaching and learning pedagogy that has been used widely in school but there is limited information on instructors’ perceptions of CL nor observations of how CL is implemented in higher education settings. In this study, we investigated the ad-vantages and challenges of embedding CL into instructors’ teaching in Iran and Australia. Data were collected through interview and observation. Results showed that despite challenges such as the lack of familiarity of CL and how it can be implemented in university curricula, issues associated with assessment, and time constraints, CL created an interactive, pleasant and safe environment for deep learning in both countries. The findings showed that there were challenges in Iran such as a tendency to use traditional approaches to teaching, insufficient understanding of how to establish teamwork, and a lack of up-to-date teaching resources. In Australia, changing courses, working with external students, catering for individual differences, and building positive relationships were some of the challenges of implementing CL. We believe that these challenges can be overcome if university instructors are prepared to address them.