There is a lack of data comparing postoperative pain after subxiphoid and intercostal video-assisted thoracoscopic surgery (VATS). Pain is an individual’s subjective experience and, therefore, difficult to compare between different individuals subjected to either procedure. This study assessed reported pain at six postoperative time points in the same patients receiving both subxiphoid and intercostal incisions for thoracic disease. Data from 44 patients who received simultaneous combined intercostal and subxiphoid VATS were retrospectively analyzed from August 2019 to July 2021. All patients received the same length of subxiphoid and intercostal incisions with or without drain placements. A numerical pain rating scale was administered on postoperative days (POD)-1, POD-2, POD-Discharge, POD-30, POD-90, and POD-180. Bilateral uniportal VATS was performed in 11 patients, and unilateral multiportal VATS was performed in 33 patients. In the unilateral VATS group, there were no differences in pain reported for both incisions in the early postoperative period. However, in the bilateral VATS group, subxiphoid wounds resulted in significantly higher pain scores on POD-1, POD-2, and POD-Discharge (p = 0.0003, 0.001, and 0.03, respectively). Higher late (3 and 6 months) postoperative pain was associated with intercostal incisions in both groups, as previously reported, whereas higher early (day 1, 2, and discharge) postoperative pain was more associated with subxiphoid incisions than intercostal incisions in the bilateral VATS group.