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Background Prevention of mother-to-child transmission (PMTCT) of HIV remains a global public health priority aimed at eliminating paediatric HIV infections and improving maternal health outcomes. The WHO advocates a comprehensive four-pronged approach: primary prevention of HIV among women of reproductive age, prevention of unintended pregnancies among women living with HIV, prevention of HIV transmission from mothers to infants and provision of treatment, care and support to women living with HIV, their infants and families. Despite significant progress in expanding PMTCT services in low- and middle-income countries, implementation challenges persist, especially in military hospital settings. Nigerian military hospitals, like others in sub-Saharan Africa, operate dual service systems for military and civilian populations, often straining available resources. Although well-organised, hierarchical command structures, frequent staff redeployments and competing operational priorities disrupt service continuity and integration with maternal and child healthcare. Consequently, programme delivery and follow-up remain inconsistent. This study explored factors that facilitate or hinder implementation of the Mentor Mothers (MMs) programme in military health facilities.Methods A descriptive exploratory qualitative design was employed to examine PMTCT implementation through the MMs programme in three military hospitals in Abuja. 18 participants were purposively selected, including three physicians, 3 PMTCT focal nurses, 6 MMs and 6 patient participants enrolled in PMTCT care. Data were gathered through six key informant interviews and two focus group discussions. Thematic analysis (TA) was used to identify patterns and relationships within the data.Findings Facilitators of effective PMTCT implementation included strong peer support networks, improved confidence among MMs, ongoing training and supervision, effective facility leadership and positive nurse–client relationships. Key challenges identified were fear of stigma leading to non-disclosure, limited male partner involvement, cultural barriers and intermittent gaps in resources and programme monitoring.Conclusion The MMs programme enhances PMTCT adherence and psychosocial support in Nigerian military hospitals. Achieving sustained impact requires stigma reduction, male partner engagement, strengthened supervision and institutionalised mentorship to advance Nigeria’s elimination of mother-to-child transmission goals.