The current study was conducted to identify the perceived effectiveness of online learning systems for urban and rural students of higher education institutions in Pakistan. A survey of 592 students from ten public and private sector institutions in Pakistan was conducted to obtain their opinions against eleven factors of perceived learning effectiveness including goal setting, time management, environmental structure, help-seeking, self-evaluation, attitude towards blended learning, technology quality, learning motivation, level of student interaction and grade average of students for two (online and face-to-face) semesters. Results indicated that there were significant differences between rural (292) and urban (300) students on the perceived effectiveness of online learning systems against all the variables including their grade performance, which were previously insignificant during online classes. The results have revalidated the social justice theory that equal opportunities and resources should be provided to all on an equitable basis to achieve the results of any social activity including online education, which is the contribution of the current research. The research has discussed several implications for policymakers, higher education institutions, and researchers in detail. Keywords, Higher education institutions, Goal setting, Attitude towards blended learning, Learning effectiveness, Technology quality.