Introduction: Health-care associated infections (HAI) are a significant problem in Neonatal Intensive Care Unit (NICU) due to associated high neonatal morbidity and mortality. Despite the presence of standard quality guidelines of infection control (SQGIC) in NICUs in Egypt, there is no adequate information about compliance of hospital staff to such SQGIC. The objective of the study is to explore the Infection Control (IC) management system and practices at the implementation level through Health Care Workers (HCWs) and to identify the performance in IC related to neonatal care procedures. METHODS: The study design was an operations research- exploratory cross-sectional study that included qualitative and quantitative data. Qualitative data were derived from in-depth interviews and focus group discussions with the hospital staff at all levels. Quantitative data were collected in a standardized checklist for each of the 22 incubators. The total patient-contacts during four well-defined sessions, daytime and night shifts had represented the sample units for statistical analysis. RESULTS: Embaba General Hospital has well-organized institutionalized system for infection control (IC). The NICU setting has satisfactory resources. Out of the total observed 291 observed patient-contacts, 61% were done by nurses. Performance in hand hygiene was scored as poor (67%) before patient contact and good (84% for low and high risk contacts) after patient contact (p=0.00). Compliance to standard was scored as good in hand washing (82%), poor in cannula insertion (74%) and good in IV fluid preparation (87%). Specialists reported excellent (100%) performance score in IC in umbilical catheter insertion. The study concluded the presence of a gap between IC hospital management and HCWs in NICU due to lack of constructive supervision especially during night shifts.