The significant time that learners spend on using e-learning media for teaching learning purpose at schools and homes creates some thought provoking questions like how the use of e-learning media may influence cognitive skills enhancement?, and if it does have influence, then how much? The study evaluates the effects of e-learning media on cognitive skills enhancement of science students respectively, and compares the impact of elearning media on cognitive skills enhancement of male and female science learners. The study is experimental in nature. Results of the study are tested at significance level alpha: a = 0.05. After conducting pre-tests, treatment and post-tests, it is found that the post-test results of male and female science students are better than their pre-test. It is also found that the cognitive skills enhancement score of both genders of students of experimental group is higher than the score of both genders of students of control group on the basis of post-tests scores. It is also found that there was no difference between cognitive skills enhancement score of male students of experimental group and that of female students of experimental group on the basis of post-tests scores. Consequently, it is concluded that the use of e-learning media has considerable positive effect on the achievement of male and female science students and it enhances their cognitive skills, but no considerable difference was observed between the cognitive skills enhancement of male and female students using e learning media.