The purpose of this study was to explore factors contributing to low achievement of learners in chemistry at ordinary secondary section in Uganda. A qualitative research approach with a case study design was applied. The sample size had twenty-two participants made up of ten females and twelve males in the following categories: one head teacher and one chemistry teacher purposively selected, ten old students sampled using snowball sampling technique and ten current senior three learners selected using simple random sampling method. Findings showed that there were several factors contributing to low achievement of learners: categorized as school factors, and learner factors. The school factors were: poorly equipped smaller laboratory making the teachers teach chemistry theoretically not practically and also the teachers fail to use the environment in teaching and learning of chemistry, smaller library with few textbooks for chemistry, few chemistry teachers, inadequate ICT services, inadequate preparation by the teachers, learner factors include: negative attitude of learners, missing lessons, negative peer influence and poor health of learners. The new findings include: teachers fail to use the environment in teaching and learning of chemistry, inadequate preparation by teachers, and negative peer influence. The study recommends that government needs to recruit more chemistry teachers and improve classroom, laboratory, and library facilities, the school administration needs to provide bursaries and guidance for learners and teachers need to teach practically and use the environment to teach chemistry.