The study is a qualitative research. It is intended to sensitize our educational system on the need to create equal learning opportunities for male and female students in the classroom. A total of 240 subjects were selected randomly among junior secondary school year three students out of nine secondary schools in Ikere local government area of Ekiti State. Three groups, A, B and C were involved. in the study, group A that comprised of male and female students. B comprised of male student only and C comprised of female students only. The instrument used was Integrated Science concept test (ISCT) which was administered on the population after three weeks intensive coaching. The results of pre test and post test were subjected fo mean, standard deviations and analyses of covariance. The two hypotheses were rejected at 0.05 alpha level of significance. It was therefore concluded that there was a significant difference between the post test mean scores of integrated science concept test (ISCT) of male and female students in the same classroom and those in different classrooms.