The present study examined whether gender, ethnicity, instructional medium and school category differences manifest in science performance and motivation to learn science among secondary school students in Sri Lanka. The mean of five successive term test scores was used as the measure of science performance. Level of motivation in terms of six dimensions was measured by using the Science Motivation Questionnaire. A sample of 1316 grade 11 students representing Sinhala, Tamil, and Muslim ethnic groups from the three categories of public schools, which provide instructions in the vernacular languages of Sinhala or Tamil, participated in the study. Girls showed significantly higher performance in science compared to boys, and there was a significant gender difference in the levels of motivational dimensions in favor of girls. Although Tamil medium students possessed a higher level of motivation to learn science, Sinhala medium students outperformed their Tamil medium counterparts in science performance. Significant differences in science performance between Sinhala, Tamil, and Muslim students were also observed. However, motivation towards learning science between Tamils and Muslims was not significantly different. Highly significant differences in both motivation to learn science and performance in science were found between three categories of schools. The present study provides information to education officials who have to achieve equity across gender, ethnicity, medium of instruction, and school category, teachers who deliver the subject and school principals who design academic support programs.