Background: Previous studies of urban school-based health centers (SBHCs) have shown that SBHCs decrease emergency department (ED) utilization. This study seeks to evaluate the effect of SBHCs on ED utilization in a rural setting. Methods: This retrospective, controlled, quasi-experimental study used an ED patient data set from the Bassett Healthcare Network in rural New York to compare ED visits between school-aged children from 12 SBHC schools before and after the SBHC opening. Time series analysis was used to determine trends in SBHC schools and 2 control schools without SBHCs over the 18-year study period. Results: ED visit incidence densities for all 12 school districts combined showed a significant increase in ED visits post-SBHC (Rate ratio (RR) = 1.15; p < 0.0001). This increase may, in part, be explained by the upward trend of ED visits in the region, as seen in the small, but significant, positive slope (RR = 0.0033, p < 0.0001) for control schools. There was variation in the change in incidence density post-SBHC among school districts, with increases in 78% of schools. Conclusions: The opening of SBHCs in rural settings results in a slight, but significant, increase in ED use, which is contrary to previous cross-sectional studies in urban settings.