Background The rates of resection of nonmalignant lung nodules suspected preoperatively to be lung cancer vary widely and are reported to be as high as 40%. We determined the impact of the frequent use of computed tomography (CT)-guided fine needle aspiration (FNA) on the resection rate of nonmalignant nodules and frequency of resections of benign disease among patients undergoing evaluation for lung cancer resection operation in an academic medical center. Methods Eligible patients underwent CT-guided FNA, surgical resection, or both during the 12-month period between July 2013 and July 2014 for known or suspected first primary resectable stage I–III lung cancer. Patient data were extracted from the electronic medical records. Results One hundred ninety-seven patients underwent surgical resection; among them the overall resection rate of nonmalignant lesions was 13.1% (26/197). For those with preoperative FNA, the rate was 7.9% (11/139), and for those with no biopsy, the rate was 25.9% (15/58) (p = 0.001). The sensitivity and specificity of FNA biopsy were 96% and 98%, respectively. The false-negative rate was 3.9% (5/128). Conclusions The resection rate of nonmalignant nodules was significantly lower for patients with preoperative CT-guided FNA biopsy than in those without. The diagnostic accuracy of FNA in these patients at moderate to high risk for lung cancer is higher than that of positron emission tomography, with a low rate of adverse events. These findings suggest that the frequent use of preoperative diagnostic confirmation by FNA results in a low rate of nonmalignant resection.