Neonatal sepsis is a leading cause of neonatal mortality. Congenital heart disease accounts for additional risk of sepsis in neonate. Here we report a case of Down’s syndrome with late onset neonatal sepsis associated with multiple superficial skin abscesses simulating staphylococcal infection. The baby was empirically treated with vancomycin. Subsequently, multidrug resistant Klebsiella pneumoniae was detected from both pus and blood culture. Change to appropriate antibiotic resulted in clinical recovery. Although sepsis is one of the major ailments in neonates, atypical presentations of neonatal sepsis in Down’s syndrome patients are underreported. Here we highlight the atypical presentation of Klebsiella sepsis and the importance of early antibiogram in such cases.