Necrotizing enterocolitis (NEC) is an inflammatory disease with evidence of increased production of proinflammatory cytokines in the intestinal mucosa. Lactobacillus reuteri DSM17938 (LR17938) has been shown to have anti-inflammatory activities in an experimental model of NEC. Activated effector lymphocyte recruitment to sites of inflammation requires the sequential engagement of adhesion molecules such as CD44. The phenotype of CD44⁺CD45RB^lo separates T effector/memory (Tem) cells from naïve cells (CD44^-CD45RB^hi). It is unknown whether these Tem cells participate in the inflammation associated with NEC and can be altered by LR17938. NEC was induced in 8-10-day old C57BL/6J mice by gavage feeding with formula and exposure to hypoxia and cold stress for 4 days. Survival curves and histological scores were analyzed. Lymphocytes isolated from mesenteric lymph nodes (MLNs) and ileum were labeled for CD4, CD44, CD45RB, intracellular Foxp3, and Helios and were subsequently analyzed by flow cytometry. LR17938 decreased the mortality, and incidence and severity of NEC. The percentage of Tem cells in the ileum and MLNs was increased in NEC but was decreased by LR17938. Conversely, the CD4⁺Foxp3⁺ regulatory T cells (Tregs) in the intestine decreased during NEC and were restored to normal by LR17938. The majority of the Tregs preserved by LR17938 were Helios⁺ subsets, possibly of thymic origin. In conclusion, LR17938 may represent a useful treatment to prevent NEC. The mechanism of protection by LR17938 involves modulation of the balance between Tem and Treg cells. These T cell subsets might be potential biomarkers and therapeutic targets during intestinal inflammation.