Emergency departments have different strategies concerning the use of computed tomography (CT) for diagnosing appendicitis. We explored the association between CT utilization rates and the negative appendectomy rates in patients with suspected appendicitis at three medical centers. A retrospective multi-center comparative study was conducted to determine the association between CT use and negative appendectomy rates at three different medical centers. Standardized extraction of data from medical records and operative reports was performed by trained investigators. Of the 339 patients included, 242 (71.4%) were imaged with abdominal CT before appendectomy (CT group), whereas the remaining patients were not (non-CT group). Thirty-six of the 339 patients (10.6%) were found to have negative appendectomies. The CT group had a significantly lower negative appendectomy rate than the non-CT group (6.6% vs. 20.6%, respectively, p < 0.05). The three centers had significantly different rates of CT utilization for diagnosing acute appendicitis (86.9%, 66.4%, and 13.3%, p < 0.05). These three centers also had significantly different negative appendectomy rates (2.5%, 16.8%, and 23.3%, p < 0.05). There was a significant inverse correlation (rho = -1, p < 0.05) between CT utilization rates and negative appendectomy rates. The rate of negative appendectomies in this retrospective study was inversely related to the rates of CT imaging before exploration in Emergency Department patients with suspected appendicitis.