Teachers constantly face the challenges of finding and applying the most effective methods of instruction that could enhance academic achievement and match the diversity among students. This study aimed at examining the effects of metacognitive and cooperative learning strategies on achievement in science classrooms. A quasi-experimental design involving 3 groups namely, two treatment groups-- cooperative learning(CL) group a metacognitive instructions(MI) group and a control group, was adopted. The study lasted for 11 weeks. A researcher-made achievement test in the topic ‘Human Anatomy’ was used to measure achievement in the 3 groups. Results revealed that the metacognitive instructions were most effective in enhancing academic achievement. Multiple regression analysis shows that there is significant relationship between metacognitive awareness and achievement. The researcher recommends that metacognitive instruction be adopted regularly in the classroom so as to help students learn material more efficiently and enhance academic achievement.