This qualitative phenomenological study aimed to explore middle school students' perceptions of using the school-based cooperative problem-based learning (SB-CPBL) approach in learning science. The study explored how SB-CPBL differs from the students' usual learning, how the new approach affects their learning process, and what are the main challenges of learning via SB-CPBL. The study elucidates the pattern of students' perceptions changes towards using SB-CPBL in learning science. The study sample consisted of two sections of eighth-graders; males (28 students) and females (32 students), with a total of 60 students, aged 14-15 years old from the King Abdullah II School for Excellence in Jordan. The study conducted semi-structured group interviews with each gender class using their native language (Arabic), and semi-structured individual interviews with the teacher and students. Findings suggested that the students' response at the final stage includes that SB-CPBL is enjoyable, attractive, and initiates the urge to think critically. However, some negative perceptions and a sense of anxiety were also shown during the initial stage.