Implementation research (IR) facilitates health systems strengthening and optimal patient outcomes by generating evidence for scale-up of efficacious strategies in context. Thus, difficulties in generating IR evidence, particularly in limited-resource settings with wide disease prevention and treatment gaps, need to be anticipated and addressed. Nigeria is a priority country for the prevention of mother-to-child transmission of HIV (PMTCT). This paper analyses the experiences of four PMTCT IR studies in Nigeria, and proffers solutions to major challenges encountered during implementation.