Locating small, non-palpable lung tumors during video-assisted thoracoscopic surgery (VATS) is difficult. In this paper, we report a simple method to identify such tumors during VATS, using intraoperative computed tomography (IO-CT). From 2015 to 2017, we performed IO-CT scans for patients who preoperatively seemed to have non-palpable lung tumors. We initially tried to locate these tumors by finger palpation through the thoracoscopic ports. IO-CT scans were performed after marking tumors with metal clips. However, difficult-to-palpate tumors were marked by initially locating the intercostal muscle from preoperative CT. Metal clips were applied just under the intercostal muscle, and IO-CT scans were performed. After locating the tumor in relationship to the marking clips, patients would undergo wedge resections during VATS, using surgical staplers. We used this procedure on 21 tumors in 18 patients, including 9 non-palpable tumors and 12 palpable tumors (mean tumor size: 7.3 mm; mean distance from pleura: 6.8 mm). All tumors were identified intraoperatively, and all patients successfully underwent wedge resections during VATS, with no intra-postoperative complications. IO-CT scans after tumor marking with metal clips during VATS can accurately locate non-palpable small sized lung tumors. IO-CT scans should be indicated for tumors that are preoperatively considered to be non-palpable.