Secondary students' perceptions of learning science and mathematics have been researched internationally, but less in the global South. This study investigated Grades 9 and 10 students' experiences of learning biology, chemistry, physics and mathematics in Bhutanese secondary schools. A mixed-methods sequential design was used. First, 524 students from 7 schools completed a survey capturing their perceptions of learning in the four subject areas. Then, 82 of those respondents participated in one of the eight focus groups, exploring patterns in the survey data. Chemistry was seen as the most challenging subject, associated with memorization, poor performance, stress and fear. Biology was perceived as more interesting and less anxiety-provoking, although a need to memorize large amounts of content was common. Mathematics was polarizing, with some students finding it easier and more enjoyable, others the opposite. These findings add to the international literature on students' perceptions and experiences of science and mathematics. They inform curriculum and pedagogic change to enhance students' experiences, reduce negative perceptions and anxiety, make the choice to study these subjects in senior secondary years more appealing, and lift performance.