The purpose of this paper was to highlight the current e-learning experience in Pakistan for both male and female undergraduates within two universities. E-learning is not a new occurrence in Pakistan. A number of studies have been carried out to assess the impact on e-learning. But to date no study has focused exclusively on 'gender' in the e-learning experience and how gender differences affect the development of e-learning and how these factors can be overcome to improve the overall experience in Pakistan. This paper has identified numerous factors that affect male and female undergraduates in their e-learning experience within the two universities in Pakistan. It has measured the extent to which these factors affect gender. The paper has concluded with a number of recommendations for improving e-learning and how these differences can be overcome. This comparative study has compared and contrasted an equal number of male (150) and female (150) undergraduates in two universities in Pakistan. The data was collected through a web-based questionnaire sent to undergraduate students (studying in the ICT discipline) through a survey software (SurveyMonkey.com). This methodological approach (matched samples) was used to identify and explore 'gender differences in the e-learning experience'. The online questionnaire was adopted to collect statistical data on the matched sample (male and female undergraduates). Followed by six in-depth semi-structured interviews (three male and three female undergraduates), in order to gain a comprehensive understanding of why these e-learning experiences have occurred. This approach has enabled the author to understand why these various underlying factors have affected male and female undergraduates in terms of promoting or hindering their experience of e-learning within the university. This methodology has captured both statistical as well as the respondent's views, feelings, emotions, motivations, aspirations and so forth. The results have verified that there is great potential and scope for e-learning development in Pakistan. The analysis of the quantitative and qualitative data has highlighted several factors that affect both male and female undergraduates. However, the results have exposed a number of factors that tend to affect female students more than compared to their male counterpart. These factors identified ranged from lack of infrastructure, government support, and computer literacy to mention a few. From these results a number of recommendations have been made on how the e-learning experience in terms of gender could be improved for further university students within Pakistan. The uniqueness and novelty of this paper lies within the methodological framework adopted. No other study (to date) has conducted a comparative study of male and female students in terms of the e-learning experience. There is only a limited amount of work on e-learning and gender related factors. Findings of this study have provided an insight into the e-learning experience within Pakistan focusing on gender differences regarding the use of e-learning. This paper contributes to knowledge by beginning to fill these gaps and addressing the need for additional work.