Introduction Necrotizing enterocolitis (NEC) is a severe inflammatory disease, mostly occurring in preterm infants. The Dutch guidelines for active treatment of extremely preterm infants changed in 2006 from 26 + 0 to 25 + 0 weeks of gestation, and in 2010 to 24 + 0 of gestation. We aimed to gain insight into the incidence, clinical outcomes and treatment strategies, in three academic referral centers in the Netherlands over the last nine years. Methods We performed a multicenter retrospective cohort study of all patients with NEC (Bell stage ≥ 2a) in three academic referral centers diagnosed between 2005 and 2013. Outcome measures consisted of incidence, changes in clinical presentation, treatment strategies and mortality. Results Between 2005 and 2013 14,161 children were admitted to the neonatal intensive care unit in the three centers. The overall percentage of children born at a gestational age of 24 weeks and 25 weeks increased with 1.7% after the introduction of the guidelines in 2006 and 2010. The incidence of NEC increased significantly (period 2005–2007: 2.1%; period 2008–2010 3.9%; period 2011–2013: 3.4%; P = 0.001). We observed a significant decrease of peritoneal drainages (↓ 16%; P = 0.001) and a decrease of laparotomies (↓ 24%; P = 0.002). The mortality rate (33% in 2011–2013) remained unchanged. Conclusion The incidence of NEC significantly increased in the last nine years. The increase in incidence of NEC seemed to be related to an increase in infants born at a gestational age of 24 and 25 weeks. The percentage of patients needing surgery decreased, while 30-day mortality did not change. Level of evidence Level IV.