It is a matter of debate whether free school choice should lead to higher or lower levels of school segregation. We investigate how school choice opportunities affect school segregation utilizing geocoded Swedish population register data with information on 13 cohorts of ninth graders. We find that local school choice opportunities strongly affect the sorting of students across schools based on the parents’ country of birth and level of education. An increase in the number of local schools leads to higher levels of local segregation net of stable area characteristics, and time-varying controls for population structure and local residential segregation. In particular, the local presence of private voucher schools pushes school segregation upwards. The segregating impact of school choice opportunities is notably stronger in ‘native’ areas with high portions of highly educated parents, and in areas with low residential segregation. Our results point to the importance of embedding individual actors in relevant opportunity structures for understanding segregation processes.