Despite the implementation of a school-based sexuality education programme meant to promote learners' sexual and reproductive health (SRH), the incidence of sexually transmitted infections (STI) and teenage pregnancy is increasing rapidly in South Africa. This phenomenon can be observed in rural schools such as those in King Cetshwayo district in the Kwazulu Natal Province. We argue that it is critical to investigate the contextual factors that influence the effectiveness of sexuality education in these schools, which ultimately impacts the learners' sexual health outcomes. The paper applies an information-motivation-behavioural skills model as its theoretical paradigm for this qualitative, phenomenological study. In 2020, nine focus group interviews were conducted to gather in-depth experiences and perspectives from a purposively sampled group of learners in the study setting. The analysis of the collected data was guided by the interpretative phenomenological analysis framework. The results indicated that the religious antecedents of learners and teachers and the activities of faith-based organisations in the study setting influence the acceptance or rejection of sexuality education messages. Based on the study findings, we argue that Christianity as a colonial religion has functioned as both a barrier and an enabler of effective school-based sexuality education. Therefore, we recommend that the paradoxical effects of religion on school-based sexuality education be addressed by optimising the enhancing effects and mitigating the inhibiting effects on sexuality education programmes in the research setting. We also propose that leaders of faith-based organisations be considered critical stakeholders in the implementation of a school-based sexuality education programme, hence the need for continuous engagement.