Background Urinary tract infection is an infection affecting infants and children. The aim of this study was to determine the etiology of urinary tract infection along with their antimicrobial resistance. Methods This cross-sectional study was conducted from June 2015 to January 2016 at Siddhi Memorial Hospital, Bhaktapur, Nepal. Urine samples were first cultured on cystine lactose electrolyte deficient agar and blood agar by semi-quantitative technique, and then incubated aerobically for 18–24 h at 37 °C. The identified bacterial isolates were tested for antimicrobial susceptibility by Kirby Bauer disc diffusion technique. Results Of 1599 urine samples, 12.3% samples showed significant bacterial growth. E. coli (58.7%) was the most common pathogen, followed by Klebsiella pneumoniae (22.5%). Most of the isolates were resistant to ampicillin and co-trimoxazole, while least were resistant to amikacin and nitrofurantoin. Higher multi-drug resistance (61.9%) was observed among isolates. Conclusions E. coli and Klebsiella spp. were predominant cause of pediatric urinary tract infection in children. Higher susceptibility observed against aminoglycosides and nitrofurans make these drugs suitable in emergency.