Stenotrophomonas maltophilia (SM) infections are known to have a significant death rate in immunocompromised patients. To better understand the epidemiology of SM infections in children undergoing anticancer therapy (pediatric hematology and oncology [PHO]) or hematopoietic cell transplantation (HCT) from 2012-2019, a large-scale, multicenter study was conducted across the country. This study examined the incidence and outcome of SM infections, treatment regimens, and multidrug resistance. Using a competing risk analysis, researchers determined the time interval between the day of diagnosis (PHO setting) and the day of transplantation during which SM infections occurred (HCT setting). To compute how long people lived after contracting a disease, the Kaplan-Meier method was used. There were a total of 1,356 HCTs and 7,337 newly diagnosed pediatric cancer cases examined over the course of the 8-year study period. Acute leukemia diagnosis increased risk for SM infection. In HCT patients, the cumulative incidence of SM infections was similar to that of PHO patients (0.81 vs. 0.76%). The majority of SM isolates (80.8%) from both patient cohorts were susceptible to the antibiotic combination trimethoprim/sulfamethoxazole. Despite being the preferred treatment, HCT patients were less likely to recover from SM infections than PHO patients (45% vs. 85%, P=0.001, log-rank test). Independent risk factors for death were the transplant operation itself and the failure to improve despite antimicrobial treatment for 18 days. Allo-HCT patients had an identical risk of SM infections and the occurrence of resistant bacterial strains as PHO patients. The prognosis of SM infections was better in the PHO environment regardless of the antibiotics used to treat them.