Background Neonatal sepsis continues to be an important cause of mortality and morbidity in low- and middle-income countries. The identification and early treatment of infants at risk of early-onset neonatal sepsis (EONS) with empiric antibiotics is a preventive strategy. Objectives To study the use of empiric antibiotics in infants at risk for EONS and assess their outcome in terms of the development of sepsis, mortality, and duration of hospital stay. Materials and Methods This retrospective cohort study was done at the Special Newborn Care Unit, GMC Thrissur. The data of babies at risk of EONS over a period of 3 years (2020–2022) was collected. One thousand two hundred and thirty-two babies with at least one risk factor for sepsis, as defined by the National Neonatology Forum (NNF) 2021 guidelines, were enrolled in the study. The antibiotic prescription pattern and the outcomes were measured. Results Empirical antibiotic treatment was received by 61.2% (754/1232) of infants, and of those, 39.5% (298/754) developed EONS. Infants treated with Piperacillin/Tazobactam and Amikacin had a higher incidence of sepsis and mortality than those started on Ampicillin and Gentamicin ( p < .001). In infants less than 32 weeks, the incidence of sepsis increased significantly with increase in number of risk factors ( p < .001). Infants with lower birth weight and gestational age were more susceptible to developing sepsis ( p < .001). EONS was significantly associated with neonatal resuscitation, umbilical vein catheterization, and invasive ventilation ( p < .001). Infants who received empirical antibiotics had a longer hospital stay, with a mean duration of 4.38 days more compared to the no antibiotics group. Conclusion In infants at risk of EONS, the empirical use of antibiotics alone did not show a favorable effect on the incidence of EONS or sepsis-related mortality.