Background: While caregiver and health system factors are known to influence paediatric ART outcomes, their roles within routine rural South African settings remain insufficiently characterised. Aim: The aim of this study is to assess the association between caregiver-mediated ART adherence, perceived healthcare access and service quality with viral suppression among children receiving ART in a rural South African province. Methods: A cross-sectional study was conducted among 86 children aged <15 years receiving ART in routine paediatric HIV care. Viral load suppression was defined as <1000 copies/mL. Predictor variables included caregiver-reported adherence (30-day recall; adherent vs. non-adherent), perceived healthcare access and perceived service quality. Associations were assessed using Chi-square or Fisher’s exact tests, where appropriate. Effect sizes were estimated using risk differences. Results: Overall, 77.9% of the child participants were virally suppressed. Caregiver-reported adherence was significantly associated with VLS (p = 0.034). The probability of viral suppression was 100% among adherent children compared to 73.2% among non-adherent children (risk difference: 26.8 percentage points). Caregiver-reported adherence demonstrated high specificity (100%) and positive predictive value (100%) but low sensitivity (22.4%) and negative predictive value (26.8%), indicating that while reported adherence reliably identified children who were suppressed, non-adherence did not consistently predict virological failure. Perceived healthcare access (p = 0.372) and service quality (p = 0.267) were not significantly associated with viral suppression. Conclusions: Caregiver-mediated adherence was strongly associated with viral suppression, whereas perceived health system factors were not independently associated with treatment outcomes in this cohort. These findings should be interpreted cautiously given the cross-sectional design and reliance on short-term adherence measures. Strengthening household-level adherence support is critical for improving paediatric HIV outcomes in rural settings.