Despite considerable efforts to reduce under-five mortality nationwide, Nigeria has fallen short of achieving the Millennium Development Goals (MDGs) target of 67 deaths per 1,000 live births by 2015. Of all the documented factors of under-five mortality, little evidence exists on the impact of systemic barriers and individual factors (maternal health-seeking behaviour) on under-five mortality in Nigeria. The study used a nationally representative sample from Nigeria Demographic and Health Survey (NDHS) 2013 dataset. The target population was 20,192 women aged 15-59 years who had given birth to 31,480 children five years before the survey. Stata software was used for data analysis. The risk of death was estimated using Cox proportional hazard models and results are presented as hazards ratios (HR) with 95% confidence intervals (CI). Findings from the overall Model I-IV revealed individual factors (maternal health-seeking indicators) as significant factors of under-five deaths (p < 0.05). Children whose mothers received antenatal care coverage (ANC) outside health care facilities (HCF) (HR: 1.60, CI: 1.0-2.4, p < 0.05); or delivered outside HCF (HR: 1.02, CI: 0.7-1.5, p < 0.05) had elevated hazard risk of death before age five. Conversely, children who were presented for postnatal check within two weeks of delivery (HR: 0.60, CI: 0.5-0.8, p < 0.05), or delivered within the longer birth interval (HR: 0.67, CI: 0.6-0.8, p < 0.001) had significantly lower hazard risk of death before age five. As part of systemic factors, children whose mothers were covered by health insurance scheme had significantly (HR: 0.52, CI: 0.2-1.2, p < 0.001) lower risk of death when compared with their counterparts without health insurance coverage. The study emphasized the need to revitalize strategies and programs to improve women health seeking behaviour and investment in the health sector through health insurance, infrastructure, and supplies.