Lack of pediatric triage and emergency care system in peripheral healthcare centers leads to unnecessary referral of low- and medium-risk patients. This study was conducted to study the risk factors predicting mortality within 48 h of admission in neonates and under-five children referred to the pediatric emergency of a tertiary care hospital in India. This prospective study was conducted on children (0-5 years) referred to the pediatric emergency who were enrolled and followed up. The outcome was defined as "survival" or "death" at 48 hours. Logistic regression analysis was conducted to assess the predictors of early in-hospital mortality. A total of 246 consecutive pediatric (62 neonates, 52 young infants, and 132 children aged 1-5 years) referral cases were enrolled; mortality within 48 hours was 20%. Lack of pediatric intensive care (odds ratio [OR] 4.07, 95% confidence interval [CI] 2.0, 8.32, P = 0.02), lack of neonatal intensive care (OR 2.10, 95% CI 1.01,4.28, P ≤ 0.001), distance from referral center >20 km (OR 4.61, 95% CI 2.01, 10.58, P = 0.0003), >1 h taken during transport (OR 7.75, 95% CI 2.93, 20.46, P < 0.001), lack of ambulance facility (OR 0.04, 95% CI 0.009, 0.143, P < 0.0001), very sick condition on arrival (OR 210.1, 95% CI 12.1, 3643.41, P = 0.0002), and unstable temperature-oxygenation-perfusion-sugar on arrival were the independent risk factors predicting in early in-hospital mortality. Developing a pediatric triage and monitoring system, tele-pediatric intensive care unit, regionalizing referral-back-referral services with robust interhospital communication, and strengthening pediatric emergency services are the need of the hour to reduce early in-hospital mortality.