Background/aim: The aim of this study was to investigate the therapeutic effect of intestinal trefoil factor (ITF) on necrotizing enterocolitis (NEC) by observing the pathological changes and detecting the protein level differences in Caspase-3, Bax, and Bcl-2 in an NEC neonate rat model. Materials and methods: A Wistar rat model of NEC was established and 30 one-day-old neonate Wistar rats were randomly divided into three groups including a normal control (group A), NEC rats treated with 0.2 ml physiological saline through intraperitoneal (i.p.) injection (group B), and NEC rats treated with 0.2 mg ITF by i.p injection (group C). Results: Compared with group B, there were statistically significant differences in Caspase-3, Bax, and Bcl-2 levels in groups A and C (P < 0.05). Moreover, there was a significant difference in the Bcl-2 level between groups A and B (P < 0.05). Conclusion: ITF alleviated injury of the intestinal tract in neonate rats with NEC and this mechanism was possibly related to a reduction in the expression of Caspase-3 and Bax and the increase in Bcl-2 expression.