The current study aims to report the effects of cooperative learning method on students` academic performance in the subject of Science and to identify the challenges if any while implementing cooperative learning in Pakistani classroom. The Researchers adopted quantitative approach and Quasi-experimental research design was employed. Experiment was conducted in a government girls’ elementary school and lasted for 13 weeks. Experimental group received treatment and was taught with cooperative learning whereas control group left untreated and was taught with traditional lecture method. The findings of the research study suggested that use of cooperative learning significantly affected students` test scores in the subject of science. Data analysis revealed that students of experimental group performed significantly better than control group in posttest. During experiment few challenges were observed such as teachers` belief, classroom furniture, lack of learning resources etc. Study strongly recommends the use of cooperative learning in classrooms to increase students` academic performance and orientation of innovative teaching methods in pre-service and in-service teachers training programs.