Introduction and objective Telemedicine has reinforced its position as a means for the continuity of healthcare services and a cost-effective approach to improving health equity as demonstrated during the COVID-19 pandemic. The preparedness of health systems for telemedicine is an indicator of the scalability of their services, especially during catastrophes. We aimed to assess the maturity and preparedness of federally funded tertiary health institutions in Nigeria, to deploy telemedicine as such data are currently lacking and are required to drive improvements in health services delivery. Methods We conducted a cross-sectional survey of thirty randomly selected federally funded tertiary health institutions in Nigeria using the Pan American Health Organization's tool for assessing the maturity level of health institutions to implement telemedicine between 17 September 2020 and 1 September 2021. Descriptive statistics were used for overall maturity levels and non-parametric tests to compare scores for overall maturity and specific Pan American Health Organization domains per region. The level of significance was set at p-value <0.05. Results The response rate was 77.4% (24 of 30 randomly polled federally funded tertiary health institutions responded). Overall, the median telemedicine maturity level was 2.0 (1.75) indicating a beginner level. No significant inter-zonal difference in the median overall maturity level ( p = 0.87). The median maturity levels for telemedicine readiness in specific domains were organizational readiness – 2.0 (2.0), processes 1.0 (1.0), digital environment 2.0 (3.0), human resources 2.0 (1.0), regulatory issues – 1.5 (1.0) and expertise 2.0 (2.0); mostly at beginner level, with no inter-zonal differences. Most participating institutions had no initiatives in place for domains of processes and regulatory issues. Conclusions The current telemedicine maturity level of federally funded tertiary health institutions in Nigeria is at the beginner level. This behoves policy-makers to advance the implementation and deployment of telemedicine nationwide as part of digital quality healthcare, to improve health equity and to ensure continuity of healthcare services in the event of another pandemic.