The extensive reforms of Sweden's education system during the last few decades have resulted in deregulation and individualization of schools. In upper secondary education, a distinct flexible course structure with multiple options was introduced in order to enhance school effectiveness and equity. This study departs in some of the previously outlined tensions in educational research between market interests and a 'free choice discourse' in relation to processes of differentiation. The purpose of this article is to investigate the ways gender patterns may be reproduced in relation to the emergence of multiple options and the re-organization of subject matters within Swedish upper secondary science, technology, engineering and mathematics (STEM) education. Our case addresses relations between discourses of choice and gender articulated in policy incentives, and large-scale enrolment patterns. Our results show how multiple options reproduce gender orders by 1) changing the system in accordance with a general market logic emphasizing 'freedom of choice', and 2) distinguishing predominantly gendered subject matters. Also, our results point to the importance of studying the STEM domain at a non-aggregated level to further understand the mechanisms behind gender gaps in STEM education.