A 38-year-old man, who had undergone surgery for gastric cancer one year previously, was found to have two pulmonary nodules (PNs: 10 mm in diameter) on chest radiography. Computed tomography (CT) revealed one of these nodules to be located near the B6b in the right lung hilus, while the other was located in the superficial region of the left lower lobe. Video-assisted thoracic surgery (VATS) was performed, for both diagnostic and therapeutic purposes. In this procedure, after preoperative CT-guided marking, simultaneous subsegmental resection of the right S6b and VATS wedge resection of the left lower lobe were performed successfully with adequate surgical margin. Histological diagnosis was compatible with metastatic pulmonary tumor from a gastric carcinoma primary. This case demonstrates that preoperative CT-guided localization can facilitate safe VATS subsegmental resection of a small deep pulmonary nodule.