Stem achievement is a predictor of national development since it empowers students with skills and capacities to confront challenges such as climate change, global warming, and unemployment. However, despite its significance and international priority, students' STEM performance has deteriorated in Bhutan. This study aimed to investigate stem subjects' performance and impeding factors by comparing the academic performance of boarding and day students in stem subjects. A convergent parallel mixed-method study was conducted with 301 participants comprising 281 students, 12 parents, and eight teachers in four secondary schools at Lhuentse. The research indicated a statistically significant difference in academic performance between boarding and day students in stem subjects, with day students outperforming boarding students. In addition, day students' self-efficacy was significantly higher than boarding students. Moreover, students' self-efficacy correlated significantly with academic performance in STEM subjects. Some of the recommendations are: to notify the need to upgrade physical structures such as hostels and bathrooms; to inform a proper use of available resources to enable students to use them for studying stem subjects; and to encourage guardians to support students in terms of resources and guidance to perform better academically in stem subjects.