This study compared the effects of Individualised Instructional Strategy (IIS) and Cooperative Learning Instructional Strategy (CLIS) on male and female senior secondary school students' academic achievement in Organic Chemistry. The study was guided by 2 research questions and 3 null hypotheses. The design was quasi-experimental. The population comprised 3,366 senior secondary class two (SS2) chemistry students. A sample of 602 students from 6 schools (339 males and 263 females) was drawn from the population using balloting technique. The experimental groups were taught with IIS and CLIS while the control groups were taught with Lecture method in each of the sampled schools. Both the experimental and control groups were taught Organic Chemistry by their regular chemistry teachers. The instruments used for the study were Chemistry Achievement Test on Organic Chemistry (CATOC), Cooperative Learning Instructional Manual and Learning Activity Package Manual, which were validated by three experts. The reliability of the CATOC was determined using KR20 with index of 0.82. The research questions were answered using mean with standard deviation while the null hypotheses were tested using Analysis of Covariance. The findings revealed that both IIS and CLIS significantly enhanced students' achievement in Organic Chemistry better than the Lecture method. However, the CLIS was more effective than the IIS. The researcher recommended among others, that chemistry students should be exposed to student-centred and activity-based teaching strategies such as the Individualised Instructional Strategy and Cooperative Learning Instructional Strategy, for enhanced students' academic achievement.