The present study examined the research question that any differences exist in school achievement among rural and urban background students with respect to instructional methods (traditional and cooperative learning strategy) used. The researcher adopted the randomized, pre-test – post-test randomised group experimental design. Total 63 students of class IX were participated in the experiment. An instrument Biology Achievement Test (BAT) was developed by researcher comprising of 100 items was used. Its reliability coefficient calculated by K20 method and Cronbach reliability formula, which were found 0.67 and 0.83 respectively. ANCOVA were used to test the hypotheses at 0.05 levels of significance. The results revealed that the structured cooperative learning strategy (STAD method) enhanced students’ achievement in biology and findings were in favour of rural students. The study revealed that implementation of structured CLS can improve achievements of rural students and can be use as a tool to fill the gap between the inequality of achievements in rural and urban students in science classroom.