The Covid-19 pandemic has made universities in Uganda to re-think the way education is delivered in challenging situations without sacrificing the intended objectives of university education. This study investigates the perception of both students and lecturers in private and public universities towards the effectiveness of e-learning. The study followed a quantitative approach and a cross-sectional survey design. The study sample consisted of students and lecturers in the departments of the Arts and Social sciences conveniently selected based on their willingness to participate. The study objectives were 1) to investigate whether there exists a difference in perception towards e-learning effectiveness between students in private and public universities 2) to investigate whether there exists a difference in perception towards e-learning effectiveness between lecturers in private and public universities. The two-sample t-test with equal variance was used to analyse the data. The study findings revealed the existence of a significant difference in perceptions towards e-learning effectiveness between students in private and public universities (p = 0.0000 < 0.05), and between lecturers in private and public universities (p = 0.0000 < 0.05). It is concluded that the apparent differences in perception are better explained by the state of readiness to adopt e-learning by both students and lecturers in private and public universities. It is recommended that universities obtain the necessary ICT infrastructure to support e-learning, make it easily accessible, and continuously train both students and lecturers in e-learning methodologies. It is also recommended that e-learning methodologies become an integral part of the teaching-learning methodologies in universities.