In this cross sectional study (June 2016 to June 2017), we studied the isolation and molecular characterization of multi-drug resistant Escherichia coli (MDR-E. coli) from children suffering from diarrhea. For this purpose, a total of 100 fecal samples were collected with the consent of the parents/ guardians on a prescribed form. The bacterial isolation was done by employing conventional and standard microbiological procedures. Subsequently, all the isolates were identified on the basis of biochemical tests and were further characterized by amplification of 16S rRNA gene followed by di-deoxy sequencing of the amplified product. Afterwards, the isolates were subjected to antimicrobial susceptibility profiling using Kirby Bauer disc diffusion method. A total of 87 E. coli isolates were identified in the current study and majority of the isolates were found sensitive to all or few antimicrobials. However, 14 E. coli isolates were found resistance to multiple drugs including amoxicillin-clavulanic acid, ciprofloxacin, gentamicin, cefoperazone and ofloxacin, hence termed as MDR-E. coli. All of the 14 isolates were further analyzed for the identification of blaCTX-M and blaTEM genes through PCR using specific primers. This resistant was found to be associated with the presence of plasmid encoded beta lactamases genes including blaCTX-M (13/14 E. coli isolates) and blaTEM (9/14 E. coli isolates). Altogether, it was found that ESBLs harboring E. coli is potential source of diarrhea among pediatric diarrheal patients. Therefore, molecular identification and characterization of bacterial pathogens along with antimicrobial susceptibility are critical to understand MDR- E. coli infections.