The COVID-19 pandemic has caused significant disruptions to educational systems globally, with Nigerian tertiary institutions facing considerable challenges in adapting to online learning. This paper explores the impact of the pandemic on Nigeria’s higher education system, focusing on the infrastructural, pedagogical, and policy-related challenges encountered during the shift to remote instruction. It highlights the unpreparedness of many Nigerian universities to implement online learning due to limited digital infrastructure, inadequate teacher training, and student access barriers. Drawing from the experiences of institutions globally, this paper also outlines recommendations for Nigerian tertiary education, including integrating environment and health courses into curricula, strengthening environmental policies, incorporating online mental health services, scaling up teacher training for digital instruction, and promoting evidence-based research. By addressing these key areas, Nigerian universities can enhance their resilience and capacity to deliver quality education during and after future public health emergencies. The paper concludes by emphasizing the need for ongoing research and policy reform to adapt the Nigerian higher education system to emerging technologies and future crises.