Nigeria is a key target country in the global effort toward elimination of mother-to-child transmission of HIV. Low coverage of prevention of mother-to-child transmission (PMTCT) interventions, adherence, and retention-in-care rates in HIV-positive pregnant women are contributing factors to high mother-to-child transmission of HIV (MTCT) rates. In Nigeria, rural areas, served largely by primary health care facilities, have particularly poor indicators of PMTCT coverage. Mentor Mothers are HIV-positive women who serve as peer counselors for PMTCT clients, provide guidance, and support in keeping appointments and promoting antiretroviral adherence and retention-in-care. The Mother Mentor (MoMent) study aims to investigate the impact of structured Mentor Mother programs on PMTCT outcomes in rural Nigeria. A prospective cohort study will compare rates of retention-in-care among PMTCT clients who are supported by formally-trained supervised Mentor Mothers versus clients who receive standard-of-care, informal peer support. Study sites are 20 primary health care centers (10 intervention, 10 control) in rural North-Central Nigeria. The study population is HIV-positive mothers and exposed infant pairs (MIPs) (N = 480; 240 MIPs per study arm). Primary outcome measures are the proportion of exposed infants receiving early HIV testing by age 2 months, and the proportion of MIPs retained in care at 6 months postpartum. Secondary outcome measures examine antiretroviral adherence, 12-month postpartum MIP retention, and MTCT rates. This article presents details of the study design, the structured Mentor Mother programs, and how their impact on PMTCT outcomes will be assessed.