The objective of the study is to describe safety and effects of protein C concentrate (PCConc) administration in neonates with sepsis-induced coagulopathy. Eighteen neonates (12 preterm and 6 full term) aged between 1 and 28 days who have severe sepsis (n = 6) or septic shock (n = 12), with coagulopathy and acquired protein C (PC) deficiency received PCConc (i.v. bolus of 100 IU/kg, followed by 50 IU/kg every 6 h for 72 h). Platelet counts, prothrombin time (PT), activated partial thromboplastin time (aPTT), fibrinogen, D-dimer, C-reactive protein (CRP), antithrombin (AT), PC, CRP, and neonatal therapeutic intervention scoring system (NTISS) were assessed before and 24, 48, and 72 h after the study entry. According to Clinical Risk Index for Babies II score (CRIB II score), the expected mortality in preterms was 10%. After 24 h of treatment, PC activity levels increased from an average of 19% to 57%, and they were within normal limits before the last PCConc bolus. During the treatment period, a shortening of PT (P = 0.04) and activated partial thromboplastin time (P = 0.02), and an increase in antithrombin levels (P < 0.0001) were observed, along with a reduction in CRP (P = 0.005) and NTISS values (P = 0.003). No adverse events were observed. This pilot study shows that in neonatal severe sepsis, normalization of PC levels is safe and probably effective in modulating the inflammatory response and in controlling coagulopathy. However, for the potential beneficial effects of PCConc administration on morbidity and mortality, a placebo-controlled, double-blind study is required.