Background: The burden of post-neonatal mortality remains considerably high in Nigeria. This study examines the rural-urban differences in post-neonatal mortality rates (PNMR) and associated factors in Nigeria., Methods: Dataset from the 2013 Nigeria demographic and health survey, disaggregated by rural-urban residence, was analyzed. PNMR was reported using frequency tabulation, whereas, factors associated were first evaluated using Chi-Square test and further examined using multivariable logistic regression analysis., Results: A total of 30384 singleton livebirths (20449 in rural and 9935 in urban residences) in the five years preceding the survey was included in this study. PNMR in rural and urban residences were 34 (95%CI: 31 - 38) and 22 (95%CI: 18 - 26) deaths per 1000 live births (P<0.001), respectively. In rural residence, living in the South-West region reduced the odds of post-neonatal mortality by 63% (Adjusted OR [AOR]: 0.372, 95%CI: 0.187 - 0.732)). In urban residence, poor wealth index (AOR: 1.660, 95%CI: 1.024 - 2.689), living in the South-East region (AOR: 2.902, 95%CI: 1.470 - 5.726), and home delivery (AOR: 1.539, 95%CI: 1.016 - 2.330) increased the odds of post-neonatal mortality. Regardless of residence, the use of solid cooking-fuels (Rural: AOR: 2.394, 95%CI: 1.211 - 4.734; Urban: AOR: 1.912, 95%CI: 1.206 - 3.030), birth interval < 24 months (Rural: AOR: 1.880, 95%CI: 1.557 - 2.270; Urban: AOR: 1.630, 95%CI: 1.042 - 2.550) and lack of breastfeeding (Rural: AOR: 2.547, 95%CI: 2.089 - 3.105; Urban: AOR: 2.152, 95%CI: 1.496 - 3.096) increased the odds of post-neonatal mortality., Conclusion: PNMR and associated factors differ in rural and urban Nigeria. Post-neonates in urban areas had better survival chances. Intervention efforts would need to prioritize findings in this study. This article is protected by copyright. All rights reserved., (This article is protected by copyright. All rights reserved.)