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 examined how SB-CPBL differs from the students' usual learning, how the new approach affects their learning process and the main challenges of learning via SB-CPBL. The study identifies key patterns in students' perceptions of SB-CPBL in science learning. The study sample consisted of two sections of eighth-grade students, comprising 28 males and 32 females, totaling 60 students aged 14 to 15 years from a middle school 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 indicated that, by the final stage, students perceived SB-CPBL as enjoyable, engaging, and stimulating for critical thinking. However, students initially expressed some negative perceptions and anxiety, particularly regarding adapting to the new learning structure and collaborative problem-solving expectations.