Enterotoxigenic Escherichia coli (ETEC) has the potential to cause nosocomial infantile diarrhea in a hospital setting. We detected 12 ETEC serotype O128:H45 isolates from diarrheal neonates in our neonatal unit from July through October 2012. These infants developed hospital-acquired and epidemiologically related diarrhea. Pulsed-field gel electrophoresis analysis and multilocus sequence typing of these 12 isolates suggested that a specific clone of ETEC serotype O128:H45-CS21-ST2332 caused nosocomial diarrhea among neonates. Of concern, this ETEC clone strain was resistant to multiple drugs, particularly third-generation cephalosporins.