This study investigated factors influencing performance of students in chemistry in secondary schools in Borama district. Chemistry is a very important science subject and its importance in scientific and technological development of any nation is widely acknowledged. In Somaliland educational system, students' performance in chemistry at the GCSE examination was still low. Between 2011 and 2014, 67.29% of students in Somaliland failed chemistry at GCSE examination against just 32.71% who passed. Between 2011 and 2014, 70.72% of students in secondary schools in Borama district failed chemistry at GCSE examination, and only 29.66% of students passed. The study established that teaching method, [F (1, 363) = 32.056, ¿ = .000, R = .291, R2 adj. = .082], facilities, [F (1, 363) = 13.650, ¿ = .000 R = .194, R2 adj. = .035], and nature of students, [F (1, 363) = 9.434, ¿ = .002, R = .162, R2 adj. = .024] had a significant effect on academic performance of students in chemistry in secondary schools in Borama district. The study concluded that teaching method is the most significant factor influencing performance of students in chemistry in secondary schools in Borama district.