Introduction While antiretroviral therapy (ART) coverage for pregnant women has undergone steady scale-up, Nigeria’s final mother- to-child transmission of HIV (MTCT) rate remains unacceptably high at 10%. This study aimed to determine final outcomes (MTCT rates) and their correlates among HIV-exposed infants (HEI) in nine states and the Federal Capital Territory, Nigeria. Methods This retrospective, cross-sectional study was conducted at 96 primary, secondary and tertiary health facilities supported by the Institute of Human Virology Nigeria. Data was abstracted for a birth cohort of HEI born between October 30, 2014 and April 30, 2015 whose 18–24 month final outcome was assessed by October 30, 2016. Only infants with a six-week first DNA PCR result, and a rapid HIV antibody test result at age 18 to 24 months were included. Multivariate logistic regression (adjusted odds ratios [aORs]) evaluated for predictors of HIV positivity at ≥18 months. Results After testing at ≥18 months, 68 (2.8%) of the 2,405 exposed infants in the birth cohort were HIV-positive. After a minimum of 18 months of follow-up, 51 (75%) HIV-positive infants were alive on ART; 7 (10%) had died, 5 (7.3%) were lost to follow-up and 5 (7.3%) were transferred out. Rural maternal residence, lack of maternal ART/ARV prophylaxis, mixed infant feeding and infant birth weight less than 2.5 kg correlated with an HIV-positive status for infant final outcomes. Conclusion The final HIV positivity rate of 2.8% is encouraging, but is not population-based. Nevertheless, supported by our findings, we recommend continued programmatic focus on early access to quality prenatal care and maternal ART for pregnant women, especially for women living with HIV in rural areas. Furthermore, implementation of nationwide sensitization and education on six-months’ exclusive infant breastfeeding with concurrent maternal ART should be strengthened and sustained to reduce MTCT rates.