Small-for-gestational-age (SGA) is defined as a birth weight below the 10th or below the 5th percentile for a specific gestational age and sex. Previous studies have demonstrated an association between SGA neonates and long-term pediatric morbidity. In this research, we aim to evaluate the possible association between small-for-gestational-age (SGA) and long-term pediatric neurological morbidity. A population-based retrospective cohort analysis was performed, comparing the risk of long-term neurological morbidities in SGA and non-SGA newborns delivered between the years 1991 to 2014 at a single regional medical center. The neurological morbidities included hospitalizations as recorded in hospital records. Neurological hospitalization rate was significantly higher in the SGA group (3.7% vs. 3.1%, OR = 1.2, 95% CI 1.1–1.3, p < 0.001). A significant association was noted between neonates born SGA and developmental disorders (0.2% vs. 0.1%, OR = 2.5, 95% CI 1.7–3.8, p < 0.001). The Kaplan-Meier survival curve demonstrated a significantly higher cumulative incidence of neurological morbidity in the SGA group (log-rank p < 0.001). In the Cox proportional hazards model, which controlled for various Confounders, SGA was found to be an independent risk factor for long-term neurological morbidity (adjusted hazard ratio( HR) = 1.18, 95% CI 1.07–1.31, p < 0. 001). In conclusion, we found that SGA newborns are at an increased risk for long-term pediatric neurological morbidity.