Conducted as an ethnographic examination of science teaching and learning in an Innovative Middle School in Korea, this study employs sociocultural theory to examine how structures afford and limit student participation in an innovative school designed to promote student-centered learning. Data includes teacher and student interviews, student responses to a questionnaire, classroom observations, and analysis of video recordings of ten lessons in two in two 8th grade science classes. Using structure|agency dialectic theory, we identify and describe some structures that afford and limit teacher and student agency at the micro (science classrooms), meso (school), and macro (Korean society) levels to raise some questions about current reform measures, such as innovation schools, that seek to position classroom teachers as agents for change in science education reform in Korea. Findings suggest that while teachers and school administrators play an essential role in structuring learning opportunities at the meso and micro levels, they have limited agency to address structural constraints originating at the macro-level, which can negatively impact teaching and learning in the science classroom. We offer implications for policy and practice and argue the need for more qualitative research, informed by sociocultural theory, to inform science education reform efforts in Korea.