Background: The spread of resistance to carbapenems among Enterobacteriaceae has become a major public health problem in recent years. In this study, we describe an outbreak of Klebsiella pneumoniae in the neonatal ward. First, we aimed to study the drug resistance, genetic relatedness, and transmission mechanism of carbapenem-resistant K. pneumoniae; second, we implemented infection control measures to contain the outbreak. Methods: We investigated 27 non-repetitive strains isolated from neonates and five strains cultured from around the neonatal ward. Polymerase chain reaction (PCR), the agar dilution method, and multilocus sequence typing (MLST) were used to analyze the resistance gene(s), antimicrobial susceptibility, and homology, respectively. Health-care personnel education, hand hygiene, outer gown changing, and infected patient isolation were strictly enforced. Results: Our antimicrobial susceptibility results show that all strains were multidrug-resistant. MLST and PCR results revealed that, in this study, all of the KPC-2-producing strains are Sequence Type (ST) 11 (ST11) (n = 22) and all of the NDM-1-producing strains are ST20 (n = 4) or ST888 (n = 1). The environmental strains were identified as KPC-2-positive K. pneumoniae ST11 (n = 3) and NDM-1-positive K. pneumoniae ST20 (n = 2). The percentages of isolates with the extended-spectrum-beta-lactamases CTX-M-15, blaCTX-M-14, blaTEM-1 were 9.4, 84.3, and 68.8 %, respectively. AmpC beta-lactamase genes were not detected in our isolates. Conclusions: KPC-2-positive K. pneumoniae ST11 and NDM-1-positive K. pneumoniae ST20 were associated with this outbreak. The identification of these isolates in samples from radiant warmers and nurses suggests that hospital cross-transmission played a role in this outbreak. Active infection control measures were effective for controlling this multidrug-resistant K. pneumoniae outbreak.