Background: Nosocomial Infection (NI) is one of the leading causes of short- and long-term morbidity and mortality among neonates, especially in Neonatal Intensive Care Units (NICUs). Objectives: We aimed to evaluate the epidemiology of NIs and associated factors. Methods: From March 2017 to September 2018, all the neonates who were admitted to the NICUs of Bahrami Children’s Hospital were enrolled. Nosocomial infections were identified based on the definition of CDC-NNIS. Demographic, clinical, and laboratory data of the patients were extracted from the medical records. Results: A total of 979 neonates were admitted to the NICU, of whom 60 were diagnosed with NI. The incidence of NI was 6.1 per 100 hospitalized patients. The most prevalent NI was bloodstream infection (30%), followed by pneumonia (21.7%). The most frequent presentations were respiratory distress (31.7%) and poor feeding (26.7%). Major pathogens were Gram-positive bacteria such as Staphylococcus aureus (25.7%) and Coagulase-negative staphylococci (25.7%). The mean hospital stay was 25.2 ± 20.89 days. The mortality rate of patients with NI was 16.7%. The factors associated with an increased risk of mortality among patients with NI were a lack of ventilation support, low birth weight, and WBCs with an abnormal range. Conclusions: The results of the present study showed that the incidence of NI was high, and the cultures collected from body fluids had a particular role in the diagnosis and treatment of NI. Standard infection control practices should be applied to reduce the incidence of NI and subsequent morbidity and mortality.