Healthcare-associated infections (HAI) are one of significant causes of morbidity and mortality. Evaluating risk factors associated with HAI are important to improve clinical outcomes. We aimed to evaluate the risk factors of HAI in children in a low-to middle-income country. A prospective cohort study was conducted during 43 months at a teaching hospital in Yogyakarta, Indonesia. All consecutive patients admitted to pediatric ICU and pediatric wards > 48 h were eligible. Those eligible patients were observed daily to identify the presence of HAI based on CDC criteria. The risk factors of HAI were identified. Multivariable logistic regression was used to identify independent risk factors. Total of 2612 patients were recruited. Of 467 were diagnosed as HAI. The cumulative incidence of HAI was 17.9%. In the multivariable analysis; length of stay > 7 days, severe sepsis, use of urine catheter, central venous catheter (CVC), non-standardized antibiotics, and aged < 1 year were independently associated with increased risk of HAI with adjusted OR (95%CI): 5.6 (4.3-7.3), 1.9 (1.3-2.9), 1.9 (1.3-2.6), 1.8 (1.1-2.9), 1.6 (1.2-2.0), and 1.4 (1.1-1.8), respectively. This study found that length of stay > 7 days, use of urine catheter and CVC, non-standardized antibiotic use, aged < 1 year, and had a diagnosis of severe sepsis increased risk of HAI.