Background Recently, thoracoscopic resection of pulmonary sequestration has become more common, since resection of an aberrant artery using an end-stapler is a safe maneuver in many cases. However, injury of the vessels can lead to major hemorrhage. We reported our surgical experience based on thoracoscopic surgery, with five cases of interlobar pulmonary sequestration, focusing on precautions for aberrant arterial vessels. Object and methods We performed pulmonary resections for five patients with interlobar pulmonary sequestration in a lower lobe (left, n = 4; right, n = 1) between April 2004 and May 2020. All aberrant vessels were derived from the lower thoracic artery. Two patients had a single aberrant artery and three had multiple. In four patients, these vessels were detected before surgery, and pulmonary sequestration was diagnosed in four. In one elderly patient, the aberrant vessel was overlooked, and lung cancer was suspected before surgery. Angiography or multidetector-row computed tomography was subsequently performed in four cases. The surgical plan was determined according to the location and size of the pulmonary lesion and three-dimensional images of aberrant vessels. Result In all patients, approaches were made thoracoscopically. Hemorrhage from an anomalous vessel was encountered in one case. Pulmonary resections included two lobectomies and three limited resections. Angioplasty for the root of anomalous branches was performed following pulmonary resections under converted minimal lateral thoracotomy in two cases. Conclusion Preoperative assessment of the anatomical variations in abnormal vessels is essential to achieve safe surgical procedures. According to the situation of the aberrant vessels, selecting surgical procedures with consideration of potential subsequent complications arising over a long period of time is important.