Surgical site infections (SSIs) are among the common problems associated with paediatric surgeries and significantly contribute to postsurgical morbidity and mortality. This study was conducted to assess antimicrobial prophylaxis practices and compliance rates with international guidelines in common paediatric surgical procedures. A retrospective cross-sectional study was conducted in paediatric patients aged < 18 years in whom four common surgeries (inguinal hernia, appendectomy, bariatric surgery and pancreaticoduodenectomy) were performed at paediatric wards during August 2015 to August 2016 in two tertiary care teaching hospitals. Compliance with antimicrobial prophylaxis practice guidelines (selection, timing and pattern of antimicrobial usage) was evaluated. The charts of 1152 eligible paediatric patients were reviewed. Among these, 66.5% (n = 766) were male and 33.5% (n = 386) were female, with a mean age of 8.4 years (standard deviation ± 5.6). Inguinal hernia was the most frequent surgical procedure conducted (36.3% of patients), followed by appendectomy (25.4%), bariatric surgery (21.9%) and pancreaticoduodenectomy (16.5%). Complete compliance with guidelines was observed in 11.2% of patients (129 of 1152). The choice of antimicrobial prophylaxis administration was appropriate in 380 cases (33%), with a higher rate of guideline adherence with appendectomy than with inguinal hernia, pancreaticoduodenectomy, and bariatric surgical procedures (55.8% vs 32%, 23.1% and 15.5%; p < 0.0001). The timing was appropriate in 490 patients (42.5%), with a higher rate in appendectomy (51%) than in other paediatric procedures (p < 0.0001). The majority of patients were managed with ceftriaxone (46%) or cefazolin (26.5%). A statistically significant difference was observed regarding antimicrobial prophylaxis prescribing practices in the hospitals (p < 0.0001). Low rates of adherence to guidelines in selected paediatric surgeries were observed. Increased awareness among surgeons and formulation of institutional and national antimicrobial prophylaxis guidelines are required.