Abstract Background Little is known about factors associated with carbapenem-resistant Klebsiella pneumoniae infections in pediatric patients, who are initally colonized with carbapenem-resistant Klebsiella pneumoniae. Materials and methods A retrospective case–control study was conducted involving pediatric and neonatal intensive care units throughout a five-year period (January 2010–December 2014). Clinical and microbiological data were extracted from Hospital Infection Control Committee reports and patients’ medical records. Risk factors were assessed in carbapenem-resistant Klebsiella pneumoniae colonized patients who developed subsequent systemic infection (cases) and compared to carbapenem-resistant Klebsiella pneumoniae colonized patients who did not develop infection (controls). Results Throughout the study period, 2.6% of patients admitted to neonatal intensive care units and 3.6% of patients admitted to pediatric intensive care units had become colonized with carbapenem-resistant Klebsiella pneumoniae. After a mean of 10.6 ± 1.9 days (median: 7 days, range: 2–38 days) following detection of colonization, 39.0% of the carbapenem-resistant Klebsiella pneumoniae colonized patients in pediatric intensive care units and 18.1% of carbapenem-resistant Klebsiella pneumoniae colonized patients in neonatal intensive care units developed systemic carbapenem-resistant Klebsiella pneumoniae infection. Types of systemic carbapenem-resistant Klebsiella pneumoniae infections included bacteremia (n = 15, 62.5%), ventilator-associated pneumonia (n = 4, 16.6%), ventriculitis (n = 2, 8.3%), intraabdominal infections (n = 2, 8.3%), and urinary tract infection (n = 1, 4.1%). A logistic regression model including parameters found significant in univariate analysis of carbapenem resistant Klebsiella pneumoniae colonization and carbapenem resistant Klebsiella pneumoniae infection groups revealed underlying metabolic disease (OR: 10.1; 95% CI: 2.7–37.2), previous carbapenem use (OR: 10.1; 95% CI: 2.2–40.1), neutropenia (OR: 13.8; 95% CI: 3.1–61.0) and previous surgical procedure (OR: 7.4; 95% CI: 1.9–28.5) as independent risk factors for carbapenem-resistant Klebsiella pneumoniae infection in patients colonized with carbapenem-resistant Klebsiella pneumoniae. Out of 24 patients with carbapenem resistant Klebsiella pneumoniae infection, 4 (16.6%) died of carbapenem-resistant Klebsiella pneumoniae sepsis. Conclusion Asymptomatic colonization with carbapenem-resistant Klebsiella pneumoniae in intensive care units of pediatric departments should alert health care providers about forthcoming carbapenem-resistant Klebsiella pneumoniae infection. Those carbapenem-resistant Klebsiella pneumoniae colonized patients at risk of developing infection due to carbapenem-resistant Klebsiella pneumoniae may be targeted for interventions to reduce subsequent infection occurence and also for timely initiation of empirical carbapenem-resistant Klebsiella pneumoniae active treatment, when necessary.