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This study examined learning environment perceptions and attitudes towards science as student’s transition from primary to secondary school and whether perceptions and attitudes differed according to gender. The study used a mixed-methods approach involving an explanatory sequential design with three overlapping phases of data collection. In the first two phases, two instruments were administered (to assess the learning environment and students’ attitudes) to 204 secondary school students. In the third phase, a sample (drawn from students involved in phase 1 and 2) of 42 secondary students were interviewed to provide insights into the quantitative data. Results revealed gender differences in perceptions of learning environment as well as differences in attitudes towards science as students transitioned from primary to secondary school.