Objectives: To systematically review literature and identify mother-to-child transmission rates of human immunodeficiency virus, hepatitis B virus, and hepatitis C virus among pregnant women with single, dual, or triplex infections of human immunodeficiency virus, hepatitis B virus, and hepatitis C virus in Nigeria. PRISMA guidelines were employed. Searches were on 19 February 2021 in PubMed, Google Scholar and CINAHL on studies published from 1 February 2001 to 31 January 2021 using keywords: “MTCT,” “dual infection,” “triplex infection,” “HIV,” “HBV,” and “HCV.” Studies that reported mother-to-child transmission rate of at least any of human immunodeficiency virus, hepatitis B virus and hepatitis C virus among pregnant women and their infant pairs with single, dual, or triplex infections of human immunodeficiency virus, hepatitis B virus, and hepatitis C virus in Nigeria irrespective of publication status or language were eligible. Data were extracted independently by two authors with disagreements resolved by a third author. Meta-analysis was performed using the random effects model of DerSimonian and Laird, to produce summary mother-to-child transmission rates in terms of percentage with 95% confidence interval. Protocol was prospectively registered in PROSPERO: CRD42020202070. The search identified 849 reports. After screening titles and abstracts, 25 full-text articles were assessed for eligibility and 18 were included for meta-analysis. We identified one ongoing study. Pooled mother-to-child transmission rates were 2.74% (95% confidence interval: 2.48%–2.99%; 5863 participants; 15 studies) and 55.49% (95% confidence interval: 35.93%–75.04%; 433 participants; three studies), among mother–infant pairs with mono-infection of human immunodeficiency virus and hepatitis B virus, respectively, according to meta-analysis. Overall, the studies showed a moderate risk of bias. The pooled rate of mother-to-child transmission of human immunodeficiency virus was 2.74% and hepatitis B virus was 55.49% among mother–infant pairs with mono-infection of HIV and hepatitis B virus, respectively. No data exists on rates of mother-to-child transmission of hepatitis C virus on mono-infection or mother-to-child transmission of human immunodeficiency virus, hepatitis B virus, and hepatitis C virus among mother–infant pairs with dual or triplex infection of HIV, hepatitis B virus and HCV in Nigeria.