Nigeria has roughly 230 million people, making it Africa's most populous country and the seventh largest in the world. Its healthcare system carries that weight across a federation of 36 states plus the Federal Capital Territory, each running its own health infrastructure with different budgets, staffing, and political will. If you are a researcher, a pharmaceutical company, or a global health organisation trying to work in Africa, you need to understand how the Nigerian system actually operates on the ground.
This article covers the structure of Nigeria's healthcare system, its disease profile, and the state of digital health and data infrastructure across the country.
Nigeria's Healthcare System at a Glance
Nigeria runs a three-tier healthcare delivery system. Local government areas (LGAs) manage primary healthcare, state governments handle secondary care, and the federal government is responsible for tertiary care. This structure was formalised in the 1988 National Health Policy. The framework has held, but how well it works depends entirely on where in the country you are looking.
The Federal Ministry of Health (FMOH) sets national health policy, coordinates disease surveillance, and oversees teaching hospitals and federal medical centres. The main federal agencies are the National Primary Health Care Development Agency (NPHCDA), which runs immunisation and community health programmes; the National Agency for Food and Drug Administration and Control (NAFDAC), which regulates pharmaceuticals and medical devices; and the National Health Insurance Authority (NHIA), which administers health insurance.
Nigeria spends very little on health relative to the size of its population. Government health spending typically falls between 4 and 6 percent of the federal budget, well below the 15 percent target African Union member states committed to in the 2001 Abuja Declaration. Per-capita health expenditure is roughly 70 to 80 US dollars per year, according to WHO estimates, which puts Nigeria in the lower tier of health spending even among West African nations. Out-of-pocket payments make up 70 to 77 percent of total health spending, depending on the source and year. Most Nigerians are, in effect, self-insured.
Public vs Private Healthcare Delivery
Nigeria's healthcare delivery splits between a large public system and a growing private sector. They serve overlapping patient populations, but they operate very differently.
Public healthcare runs through approximately 30,000 primary health centres (PHCs), around 4,000 secondary facilities (general and specialist hospitals), and roughly 60 tertiary institutions including university teaching hospitals and federal medical centres. On paper, the public system is the backbone of care for most Nigerians. In practice, many PHCs, particularly in rural areas, are short-staffed, have intermittent drug supply, and lack basic diagnostic equipment. Somewhere between 30 and 40 percent of PHCs are estimated to be non-functional or only partially functional at any given time.
Private healthcare picks up much of the slack. Nigeria has thousands of private hospitals, clinics, and diagnostic centres, concentrated in Lagos, Abuja, Port Harcourt, and Kano. The private sector spans single-physician clinics in residential neighbourhoods all the way to large corporate hospital groups with modern diagnostics and surgical capacity. Private providers handle an estimated 60 to 70 percent of all outpatient care in Nigeria. For international researchers and sponsors, private hospitals tend to have better electronic record-keeping and more standardised clinical workflows, especially in Lagos and Abuja.
The two sectors complement each other but coordinate poorly. Referral pathways between tiers are inconsistent, and patient records almost never follow a patient from a private clinic to a public hospital or the other way around. This fragmentation directly undermines health data quality and continuity. Digital health initiatives are starting to chip away at the problem, but progress is slow.
Disease Burden and Epidemiological Profile
Nigeria has what epidemiologists call a "double burden of disease": high rates of infectious diseases alongside a fast-growing load of non-communicable diseases (NCDs).
Infectious diseases are still the leading killers. Malaria dominates. Nigeria carries approximately 27 percent of the global malaria burden and roughly 31 percent of global malaria deaths, according to the WHO's World Malaria Report. The country ranks sixth globally for tuberculosis incident cases. HIV prevalence is approximately 1.3 percent among adults aged 15 to 49, which sounds modest until you account for the population size: nearly 1.9 million people are living with HIV, the fourth-largest HIV population in the world. Diarrhoeal diseases, lower respiratory infections, and neonatal conditions are the other major causes of death among children under five.
Non-communicable diseases are rising fast, driven by urbanisation, dietary changes, and an ageing population. Hypertension prevalence among Nigerian adults is estimated at 28 to 32 percent, but awareness sits below 40 percent and adequate control below 20 percent. Diabetes prevalence is 3 to 5 percent nationally, higher in cities. Cancer diagnoses are increasing, with breast, cervical, and prostate cancers the most common. Treatment capacity has not kept up: Nigeria has fewer than ten functional radiotherapy centres for its entire population.
This dual disease profile makes Nigeria a valuable setting for both infectious disease research and NCD management studies in low- and middle-income countries. Researchers studying co-morbidities, such as the interaction between HIV antiretroviral therapy and cardiovascular risk, can find patient populations here that simply do not exist at scale elsewhere. That connects directly to the broader argument for diversity in clinical trials.
Digital Health and EMR Adoption Across Nigeria
Nigeria's digital health environment is in transition. Unlike Rwanda, which achieved near-universal EMR coverage in its public hospital system, or Kenya, whose OpenMRS network spans thousands of facilities, Nigeria's EMR adoption has been uneven, driven by a mix of donor-funded programmes, state-level initiatives, and private-sector innovation.
Federal initiatives. The FMOH released a National Digital Health Strategy in 2021, outlining a roadmap for electronic health records, telemedicine, and data interoperability. The strategy builds on earlier investments such as the District Health Information System 2 (DHIS2), which is used across all 36 states for aggregate health reporting. DHIS2 captures facility-level indicators (immunisation coverage, antenatal care visits, disease notifications) rather than individual patient records, but it provides a national data backbone that many countries in the region lack.
Donor-funded EMR deployments. PEPFAR and the Global Fund have driven EMR adoption in HIV and TB treatment facilities. OpenMRS and similar open-source systems are operational in several hundred facilities, primarily in high-burden states across the north-central and south-south regions. These systems produce patient-level, longitudinal records that are increasingly coded to international standards. The challenge is that these deployments are disease-programme specific, a facility may have robust electronic records for its HIV patients but continue to use paper registers for all other services.
Private-sector systems. Large private hospital groups in Lagos and Abuja have adopted proprietary hospital information systems (HIS) with electronic medical records, laboratory information systems, and pharmacy modules. Some of these systems are cloud-based and produce structured, time-stamped clinical data suitable for research use. However, there is no standardised data format across private providers, and interoperability between systems remains limited.
Telemedicine and mobile health. Nigeria has seen a surge in telemedicine platforms, accelerated by the disruptions of 2020 and 2021. Platforms offering remote consultations, digital prescriptions, and chronic disease management have expanded rapidly in urban areas. While these services generate valuable encounter data, they typically capture a narrower clinical profile than facility-based EMRs, consultation notes, prescriptions, and symptom assessments rather than laboratory results, imaging, or procedural records.
The overall picture is one of rapid but fragmented progress. Nigeria has pockets of high-quality electronic health data (PEPFAR-supported facilities, leading private hospitals, telemedicine platforms) surrounded by vast stretches of paper-based record-keeping. Aggregation platforms like Kapsule play an important role in bridging these pockets, harmonising records from multiple systems into research-ready datasets that can support real-world evidence generation for regulatory and market access purposes.
Health Data Infrastructure: Where Nigeria Stands
Nigeria's health data infrastructure reflects both the country's scale and its administrative complexity. Several national systems provide population-level health intelligence, even where individual patient records remain fragmented.
National Health Management Information System (NHMIS). Managed by the FMOH and powered by DHIS2, the NHMIS collects routine health facility data from all 36 states and the FCT. Reporting completeness has improved substantially over the past decade, with many states now achieving reporting rates above 80 percent for key indicators. The data is aggregate rather than patient-level, but it is valuable for burden-of-disease estimation, programme monitoring, and health workforce planning.
Civil registration and vital statistics (CRVS). Nigeria's birth and death registration systems remain incomplete. The National Population Commission estimates that birth registration coverage is approximately 43 percent nationally, with wide variation between urban and rural areas. Death registration is even lower. This gap means that national mortality statistics rely heavily on demographic surveys and modelling rather than direct enumeration.
Disease surveillance. The Nigeria Centre for Disease Control (NCDC) operates the Integrated Disease Surveillance and Response (IDSR) system, which tracks notifiable diseases across all states. The NCDC gained international visibility during its response to the Ebola outbreak in 2014 and has since strengthened its digital surveillance infrastructure, including real-time dashboards and mobile-based reporting tools. This system is a genuine strength of Nigeria's health data ecosystem.
Health insurance data. The NHIA, established in 2022 to replace the former National Health Insurance Scheme, is working to expand coverage beyond the formal employment sector. As enrolment grows, claims data from the NHIA will become an increasingly important source of health utilisation information (diagnostic codes, treatment patterns, referral pathways), though coverage currently remains below 5 percent of the total population.
For researchers comparing health data maturity across the region, Nigeria's infrastructure shares some characteristics with Ethiopia's evolving health information systems, large-scale aggregate reporting through DHIS2, growing but incomplete EMR adoption, and a civil registration system that is still catching up to population growth.
Challenges Facing Nigeria's Health Sector
Understanding the structural challenges in Nigerian healthcare is essential for anyone planning research, investment, or programmatic work in the country.
Health workforce shortages. Nigeria produces a large number of medical graduates, but emigration, the so-called "brain drain", has accelerated in recent years. The country's physician-to-population ratio is approximately 4 per 10,000 people, well below the WHO recommended minimum of 10 per 10,000. Nurses and midwives face similar shortages, particularly in rural and northern states. The emigration of trained health workers to the United Kingdom, the United States, Canada, and the Gulf states has intensified since 2020, with some estimates suggesting that over 10,000 Nigerian doctors have relocated abroad in the past five years.
Financing gaps. As noted above, government health spending falls well short of the Abuja Declaration target. The consequence is chronic underfunding of public facilities: drug stock-outs, equipment breakdowns, delayed salary payments for health workers, and deteriorating infrastructure. Donor funding, while significant in areas like HIV, TB, and malaria, does not cover the broader health system needs.
Geographic inequality. Healthcare access varies dramatically between southern and northern Nigeria, between urban and rural areas, and between wealthy and poor states. States in the north-west and north-east (Sokoto, Zamfara, Borno, Yobe) have some of the worst health indicators on the continent, with maternal mortality ratios and under-five mortality rates several times higher than those in Lagos or Rivers State. Security challenges in parts of the north-east and north-west further restrict health service delivery and data collection.
Fragmented governance. The three-tier system means that health policy is set federally but implemented by 36 state governments and 774 LGAs, each with different capacities and political priorities. Coordination failures between tiers are common, and there is no unified patient identification system that works across state boundaries.
Data interoperability. Multiple EMR systems, proprietary hospital information systems, and paper-based records coexist with no universal data exchange standard. While the National Digital Health Strategy envisions interoperability, the practical work of connecting disparate systems across a country of this size and complexity will take years.
Opportunities for Research and Clinical Development
Despite these challenges, Nigeria offers distinctive advantages for health research and clinical development that are difficult to replicate in other markets.
Scale. No other African country matches Nigeria's population size. For studies requiring large sample sizes (rare disease research, pharmacogenomic studies, post-market surveillance), Nigeria's patient volumes are unmatched on the continent. A single large teaching hospital in Lagos may see more outpatient visits in a month than some neighbouring countries see in a quarter.
Genetic diversity. Nigeria is home to over 250 ethnic groups, each with distinct genetic profiles. This diversity is a significant asset for pharmacogenomics research, biomarker discovery, and clinical trials seeking to understand drug response variation across populations. The Yoruba, Igbo, and Hausa populations (the three largest) are already represented in global genomic databases, but hundreds of smaller populations remain largely unstudied.
Regulatory capacity. NAFDAC is one of the more developed regulatory agencies in sub-Saharan Africa, with a track record of pharmaceutical and clinical trial oversight. Nigeria is also a member of the African Medicines Agency (AMA) treaty, which aims to harmonise regulatory standards across the continent. For sponsors planning multi-country clinical programmes in West Africa, NAFDAC approval provides a credible anchor.
Growing digital infrastructure. While EMR adoption is uneven, the trajectory is clearly upward. Nigeria's technology sector (centred in Lagos) is the largest in Africa by venture capital investment, and health technology is a growing vertical. The density of technical talent means that data engineering and health informatics capacity is available locally, reducing reliance on external technical partners.
Research institutions. Nigeria has a deep bench of academic medical centres with research experience. The University of Lagos Teaching Hospital (LUTH), University College Hospital (UCH) Ibadan, Ahmadu Bello University Teaching Hospital (ABUTH) Zaria, and the University of Nigeria Teaching Hospital (UNTH) Enugu all have active research programmes, IRB infrastructure, and experience with international collaborations. Kapsule works with facility networks across Nigeria to aggregate structured health records that meet international research standards.
For organisations evaluating where to invest in African health data, Nigeria is not the easiest market. But it is arguably the most important. Its scale, diversity, and growing digital infrastructure make it indispensable for any serious research or commercial strategy on the continent.
Kapsule provides access to structured, de-identified health records covering over 75 million patients across 9 African countries. Contact our team to discuss how Nigerian health data can support your research or clinical development programmes.
This article is intended for informational purposes only and does not constitute legal, medical, or regulatory advice. Readers should obtain independent professional counsel for their specific circumstances.