Purpose: The shutdown of normal face-to-face educational method of learning caused by the coronavirus disease 2019 (COVID-19) pandemic has made the education stakeholders reconsider and rethink education anew in light of the emerging challenges and opportunities imposed on e-learning in higher education in Nigeria post COVID-19. This study investigates the challenges confronting e-learning in higher education in Nigeria amid COVID-19. Design/methodology/approach: Drawing upon data collected through a structured questionnaire administered to 395 lecturers in various disciplines in private, state and federal universities in Nigeria, the study adopts a quantitative research method. The quantitative data were analyzed using descriptive statistics. Findings: The findings indicate that Nigeria Higher Education Institutions (HEIs) are still in the early stage of adopting the e-learning mode of study. In addition, there was no existing e-learning curriculum before the pandemic. Also, adopting e-learning mode of teaching was an uphill task for both the lecturers and the learners, given the lack of experience in information and communications technology usage and inadequate infrastructure to support e-learning. Research limitations/implications: A major limitation of the study is the inability to investigate the challenges facing students in using e-learning tools due to the unavailability of access to students during the lockdown. However, the limitations create opportunities for further studies into the subject matter. Originality/value: The study is timely given that HEIs in Nigeria and some other countries in Africa are yet to adopt blended teaching methods. Literature reveals that most HEIs in Nigeria are using only brick and mortar mode of teaching despite the benefit of blended learning in a pandemic situation.