(1) Background: The relationship between enteral nutrition and neonatal necrotizing enterocolitis (NEC) among premature neonates is still unclear. The present work was designed to assess the relationship between NEC and feeding strategies compared to control infants. (2) Methods: A retrospective case-control study of premature infants (<35 weeks’ gestation) with or without NEC that examined feeding practices and clinical characteristics at birth and 3, 7, and 14-day hospitalization, with a longitudinal and cross-sectional analysis. (3) Results: A total of 100 newborns with NEC diagnosis and 92 neonates without the disease with similar demographic and clinical characteristics were included. The median day of NEC diagnosis was 15 days (Interquartile Range (IQR) 5–25 days). A significantly higher number of neonates that were fasting on days 7 and 14 developed NEC (p < 0.05). In the longitudinal analysis, generalized linear and mixed models were fit to evaluate NEC association with feeding strategies and showed that exclusive mother’s own milk (MM) and fortified human milk (FHM) across time were significantly less likely associated with NEC (p < 0.001) and that enteral fasting was positively related with NEC. In the cross-sectional analysis, a binary logistic regression model was fit and predicted 80.7% of NEC cases. MM was also found to correlate with a reduced risk for NEC (OR 0.148, 95% CI 0.044–0.05, p = 0.02), and in particular, on day 14, several factors were related to a decreased odd for NEC, including birth weight, antenatal steroids, and the use of FHM (p < 0.001). (4) Conclusions: MM and FHM were associated with less NEC compared to fasting on days 7 and 14. Feeding practices in Neonatal Intensive Care Units (NICUs) should promote exclusive MM across the two-week critical period as a potential guideline to improve NEC outcome.