Introduction: Despite major progress in antiretroviral therapy (ART) scale-up, viral suppression (VS) among children living with Human Immunodeficiency Virus (HIV) remains below global targets in Mozambique. Evidence on determinants of virological non-suppression (VNS) in decentralized rural settings is still limited. Objective: This study aimed to analyse factors associated with VNS among children receiving ART in Chokwe District, Gaza Province, Mozambique. Methods: We conducted a retrospective cohort study including children younger than 15 years who initiated ART between 2022 and 2024 in 27 health facilities in Chokwe District. Sociodemographic, clinical, laboratory, and health care data were extracted from paper medical records and electronic databases. VNS was defined as viral load (VL) [≥]1,000 copies/mL of blood after at least 6 months of ART initiation. Kaplan-Meier methods and Cox proportional hazards regression models, adjusted for key sociodemographic, clinical, and health care characteristics, were used to identify factors associated with time to VNS. Adjusted hazard ratios (aHR) and 95% confidence intervals (95% CI) were estimated.We conducted statistical analyses using the STATA 15 and R 4.5.1 software packages. Results: A total of 285 children were included. At 6 months after ART initiation, 28.2% of children presented VNS, while 23.3% presented VNS at 18 months. In the adjusted analysis for the first 6 months of follow-up each additional year of age at ART initiation was associated with lower risk of VNS, whereas not initiating treatment on the same day of diagnosis increased the risk of VNS. At 18 months of follow-up, age at ART initiation showed evidence of a non-linear association with VNS. Tuberculosis co-infection and undernutrition at 6 months were also associated with a higher risk of VNS. Conclusion: VNS remains frequent among children receiving ART in Chokwe District. Younger age during early follow-up, delayed ART initiation, tuberculosis co-infection, and undernutrition were important determinants of poor virological outcomes. Strengthening early HIV diagnosis, timely ART initiation, integrated management of TB and undernutrition, and age-responsive follow-up strategies may improve long-term virological outcomes among children living with HIV in resource-limited settings.