The use of antiretroviral therapy (ART) for HIV-1 treatment effectively suppresses viral replication if managed appropriately, but sometimes patients experience incomplete viral suppression with manifestation of either persistent low-level viremia (LLV) or discernible virological failure (VF). In the present study, potential risk factors associated with LLV and VF were investigated in a cohort of HIV-1 infected Kenyan children receiving ART. Drug resistant (DR) variants in children with or without LLV were examined using a next-generation sequencing-based HIV DR typing protocol. The potential association between HIV DR mutations (DRMs) and LLV and/or VF was then examined. To measure the potential impacts from other clinical and epidemiological confounding factors, a database comprising of epidemiological and clinical information from this patient cohort was established and sanitized for ensured accountability. Statistically significant correlations between the examined factors and LLV or VF were determined using chi-square test, Kaplan-Meier survival analysis, and Cox proportional hazard models. Of 293 examined patients, 20% had LLV and 22% of the selected patients progressed to VF with no significant association observed between LLV and VF. ART adherence during therapy, baseline CD4 counts, DRMs at LLV, WHO clinical stage, gender, ART therapy stage (1st/2nd line), ART drugs and co-morbidities were not significantly associated with LLV, whereas, the ART adherence, CD4 counts and co-infection with pneumonia was significantly associated with VF. This study highlights the factors predictive of VF, and the relevance of maintaining LLV in HIV-infected children.