The northern geopolitical zones (NGZs) continue to report the highest under-5 mortality rates (U5MRs) among Nigeria’s six geopolitical zones. This study was designed to identify factors related to under-5 mortality (U5M) in the NGZs. The NGZ populations extracted from the 2018 Nigeria Demographic and Health Survey were explored to assess the factors associated with U5M using logistic regression, generalised linear latent, and mixed models. Between 2013 and 2018, the northwest geopolitical zone reported the highest U5MR (179 deaths per 1000 live births; 95% confidence interval [CI]: 163–194). The adjusted model showed that geopolitical zone, poor household, paternal occupation, perceived children’s body size at birth, caesarean delivery, and mothers and fathers’ education were highly associated with increased odds of U5M. Other significant factors that influenced U5M included children of fourth or higher birth order with shorter interval ≤ 2 years (adjusted odds ratio [aOR] = 1.68; CI: 1.42–1.90) and mothers who did not use contraceptives (aOR = 1.41, CI: 1.13–1.70). Interventions are needed and should primarily spotlight children residing in low-socioeconomic households. Educating mothers on the benefits of contraceptive use, child spacing, timely and safe caesarean delivery and adequate care for small-sized babies may also reduce U5M in Nigeria, particularly in the NGZs.