Background: Central venous catheter (CVC) thrombosis poses a significant challenge in neonatal intensive care units (NICUs). This study aimed to assess the incidence, identify risk factors, and explore management strategies for CVC thrombosis in neonates. Methods: The prospective study was conducted from September 2021 to February 2022 in Benha University Hospital and Benha Children Hospital. The study included 150 neonates with central venous lines. In-depth assessments, including medical history, examinations, laboratory investigations, and Doppler ultrasound, were employed. Results: Among the neonates, 12% experienced CVC thrombosis, with a mortality rate of 38%. Analysis revealed significant associations between thrombosis and factors such as gestational age (P < 0.001), weight (P < 0.001), and sepsis (P < 0.001). Laboratory findings indicated higher hematocrit levels (P < 0.0001) and elevated C-reactive protein (CRP) levels (P = 0.011) in neonates with positive thrombosis. Multivariate analysis identified duration of CVC > 8.52 as the most significant factor (OR = 109.948, P < 0.001), followed by infected CVC (OR = 40.203, P < 0.001) and hematocrit level > 54.32 (OR = 15.617, P = 0.002). ROC analysis demonstrated high predictive value for both hematocrit (AUC = 0.877, P < 0.001) and duration of CVC (AUC = 0.822, P < 0.001). Conclusions: Duration of CVC > 8.52, infected CVC, and elevated hematocrit levels were identified as significant risk factors for CVC thrombosis in neonates.