Kenya ART guidelines recommend three sessions of enhanced adherence counselling (EAC) following detectable viral load. The objective of this study was to assess completion of EAC sessions and factors associated with viral re-suppression amongst adolescents and young persons (AYPs) with persistent viremia in Western Kenya. A retrospective analysis of routinely collected data abstracted from viral load registers was done. AYP with persistent viremia (consecutive viral load ≥1000 copies/ml) between October 2017 to September 2019 were followed for 12 months; those with more than one follow-up viral load results were analyzed. EAC was satisfactory if at least three sessions attended, barriers identified and addressed. Morisky scores 0 and at least 1 indicated optimal and sub-optimal adherence, respectively. Logistic regression models were used to assess predictors of viral load suppression (VLS). Of 124 AYPs with persistent viremia, 118 (95.2%) had documented follow-up viral load results and 119 (96%) completed three EAC sessions. Overall, 55 (47%) clients re-suppressed during the study period. AYPs who had satisfactory EAC sessions had higher odds of achieving VLS [odds ratio (OR) = 3.7, 95% confidence interval (CI): 1.6-8.1]. Similarly, AYPs with an optimal adherence had eight times (OR = 8.1, 95% CI: 3.5-18.5) higher odds of achieving VLS, and those who were suppressed at 6 months post-ART initiation had higher odds of achieving VLS at 12-months (OR = 2.5, 95% CI: 1.1-5.8). Satisfactory EAC sessions and optimal ART adherence was strongly associated with viral re-suppression among AYPs with persistent viremia. Continued support to EAC intervention is critical to improve treatment outcome among AYP living with HIV.