This study aims to investigate the risk factors for infection and mortality associated with carbapenem-resistant Klebsiella pneumoniae (CRKP) in hospitalized children, with the goal of providing valuable insights for the prevention and treatment of these bacterial infections. A retrospective case-control study was conducted, including 153 cases of carbapenem-sensitive K. pneumoniae infection in children and 49 cases of CRKP infection. Among the CRKP cases, 40 children survived and nine died. Logistic regression analysis was used to screen the risk factors for CRKP infection in children, establish a predictive model, and analyze the factors associated with mortality in CRKP-infected children. The results of the multivariate regression analysis showed that hematopoietic malignancies (OR = 28.272, 95% CI: 2.430–328.889), respiratory tract infections (OR = 0.173, 95% CI: 0.047–0.641), mechanical ventilation (OR = 3.002, 95% CI: 1.117–8.071), number of antibiotic agents (OR = 1.491, 95% CI: 1.177–1.889), WBC (OR = 0.849, 95% CI: 0.779–0.926), and neutrophil count (OR = 0.779, 95% CI: 0.677–0.896) were identified as significant factors associated with CRKP infection in children. Specifically, CRKP-infected children with a history of multiple hospitalizations within the past three months, blood stream infections, and decreased WBC and lymphocyte counts should be monitored closely due to poor prognosis. Underlying hematopoietic malignancies in children, non-respiratory tract infections, mechanical ventilation after admission, and use of multiple antibiotics without significant increase in white blood cell and neutrophil counts are major factors influencing CRKP infection. Particularly, CRKP-infected children with blood stream infections and no significant increase in neutrophil count should be closely monitored for potential severity of illness.