The dramatic increase of resistance in Klebsiella pneumoniae (K. pneumoniae) due to the misuse of antibiotics poses one of the greatest health threats and is a global health concern. Colistin, a last resort antibiotic is used extensively to treat carbapenem-resistant Klebsiella pneumoniae infections. Present research carried out to analyze the molecular mechanism, clonal types, and outcomes of the infections caused by colistin-resistant K. pneumoniae in neonates during an outbreak in neonate intensive care unit. Twenty-eight cases of colistin-resistant, carbapenem-resistant K. pneumoniae were identified between March and April 2016. Isolates were genotyped using multi-locus sequence typing and the molecular mechanism of colistin resistance was ascertained. All the colistin-resistant K. pneumoniae isolated from neonates during outbreak have insertional inactivation by ISL3 family transposes in the mgrB gene and were clonally related belong to ST11. PCR screening confirmed the presence of the blaOXA-48 and blaSHV-34 genes. The observed mortality was 35.7% in two-month periods. The present baseline report of colistin-resistant K. pneumoniae ST11 outbreak suggested the emergence of clones with this phenotype that required paramount importance for future health monitoring and assessment.