The purpose of this study is to investigate the factors influencing students’ higher secondary level science performance in one of the higher secondary schools of Bhutan. A total of 150 students were selected through purposive sampling. The sample includes both current classes XI and XII and former class XII graduates of the school. Through the use of mixed method research design, the data were collected using survey questionaries and interview in focus group. The quantitative data were analysed using descriptive statistics techniques and qualitative based on themes. The result of the study showed that the science performance of students were negatively affected by the inadequate support from school administration, lack of experienced and dedicated teachers and, poor supports from parents and relatives of the students. Thus, this study recommends school administration to take extra initiative towards improving students’ academic performance and teachers to explore different teaching pedagogies that can stimulate students’ interest towards learning science.