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Objective: Carbapenem-resistant Enterobacteriaceae (CR<i>E</i>) infection is life-threatening, especially for immunocompromised children. The source tracking of CR<i>E</i> could prevent bacteremia during hospitalization. In this study, the intestinal colonization of CR<i>E</i> and their translocation to blood were investigated. Methods: Stool samples from immunocompromised pediatric patients were collected after admission, and secondary stool and blood samples were collected in case of fever. After CR<i>E</i> phonotypic detection, the OXA-48, NDM-1, VIM, IMP, and KPC genes were detected by PCR. Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) was used to determine the phylogenic relatedness of the blood and fecal isolates. Results: Bacteremia was recorded in 71.4% of the patients. Enterobacteriaceae spp. were recorded in 100% of the stool samples and 31% of the blood samples. The correlation between the length of stay (LOS), days of fever, chemotherapy regimens, and death rate was significant (<i>p</i>-value ≤ 0.05). OXA-48 was present in all CR<i>E</i> isolates in both the primary and the secondary stool samples and the blood samples. According to the phylogenetic data, 58.33% of the patients with bacteremia had identical blood and stool isolates. The death rate was 24.4% in children with CR<i>E</i> bacteremia. Conclusions: The primary intestinal colonization with CR<i>E</i> in immunocompromised pediatrics and their translocation to blood was established in this study. The implementation of infection control programs and the application of infection prevention strategies for immunocompromised children is necessary.