This is a research into causes of student’s difficulty in learning basic science in Junior Secondary School in Enugu South LGA, Nigeria. The study investigated 150 secondary school students, 70 parents, 60 teachers and 20 government officials from Enugu State Ministry of Education. Five (5) research questions and one hypothesis guided the study. Separate questionnaire were used to collate data from the respondents. Frequencies, percentages, bar chat, mean, standard deviation, variance and analysis of variance were used to answer the research questions and to analyze the result from the hypothesis. The results revealed that there are insufficient qualified teachers teaching basic science related subjects in the sampled school as the percentages of the unqualified teachers constituted about 32.86%. They are either Nigeria Certificates in Education (NCE), Higher National Diploma (HND) or engineers. Although, the result revealed that students have positive attitude towards Basic science related subjects but the classes are usually overcrowded as the students are always more than 35-40 in the classes. It is also observed that lack of school materials such as textbook, poor scientific home, students poor study habit at home and above all there is inadequate funding and a significant difference in the influence of the stakeholders on students’ performance in basic science related subjects. Recommendations were made based on these findings.