Every year in Nigeria, malnutrition contributes to more than 33% of the deaths of children below 5 years, and these deaths mostly occur in the northern geopolitical zones (NGZs), where nearly 50% of all children below 5 years are stunted. This study examined the trends in the prevalence of stunting and its associated factors among children aged 0-23 months, 24-59 months and 0-59 months in the NGZs. The data of 33,682 recent live births in the NGZs, extracted from the Nigeria Demographic and Health Surveys from 2008 to 2018, were used to investigate the factors associated with stunting using multilevel logistic regression. Children aged 24-59 months reported the highest prevalence of stunting, with 53.3% (95% confidence interval: 52.0-54.6%). Multivariable analyses revealed four common factors that increased the odds of a child's stunting across all age subgroups: poor households, geopolitical zone (northwest or northeast), being a male and maternal height (<145 cm). Interventional strategies focused on poverty mitigation through cash transfer and educating low socioeconomic mothers on the benefits of gender-neutral supplementary feeding and the timely monitoring of the offspring of short mothers would substantially reduce stunting across all age subgroups in the NGZs.