The vicious spread of undesired antibiotic resistance among all the possible horizons of the living world is a cause of great concern and requires immediate attention. As we are concerned about the prevalence of these antibiotic resistance genes (ARGs), studies have suggested the presence of antibiotic resistant determinants in highly controlled environments such as neonatal-intensive care units (ICU). The presence of ARGs in the typical neonatal facilities are a kind of modern nightmare. In the present work, neonatal gut resistome from infants under ICU care was analyzed by metagenomic approach, to examine the possibility of spread of ARGs in neonatal care units. All samples were found to be rich in ARGs and were containing 176 to 291 ARGs per sample and the abundance ranging from 7.68 to 12.86 copies of ARGs per copy of the 16S rRNA gene. Among the all ARGs, Aminocoumarins (mdtA, mdtC), Aminoglycoside (cpxA, APH(3'')-Ib) and Bacitracin (BacA) were the most abundant. The analysis also found that chromosomal ARGs were having significantly higher abundance compared to plasmid ARGs (p < 0.05). We also found that ARGS were highly correlated to metal resistant genes, as compares to mobile genetic elements. Moreover, Efflux pump-based virulence factor genes were also highly associated with ARGs. While, the taxonomy of ARGs carrying contigs showed the majority of genera Klebsiella and Enterobacter. The present study showed, that the higher gut resistome in neonatal ICUs could be due to the compromised sterile conditions in the neonatal units, which present a greater risk to the neonates even in the controlled environment.