Subxiphoid thymectomy is a novel alternative to the transthoracic approach and sternotomy, with potential benefits, such as reduced postoperative pain and faster recovery. We previously reported the initial experience with subxiphoid single-port robotic-assisted thoracic surgery (SRATS) thymectomy using the single-port robotic system (SPS). However, the efficacy of this technique remains unknown. Thus, this study examined the multi-institutional experience with SRATS thymectomy and compared the perioperative outcomes of this technique to those of subxiphoid single-port video-assisted thoracic surgery (SVATS) thymectomy. The data of patients who underwent subxiphoid SRATS and SVATS thymectomy, performed by three thoracic surgeons at three institutions between September 2018 and May 2024, were retrospectively collected. In total, 110 patients were included, with 85 and 25 undergoing SRATS and SVATS thymectomy, respectively. After propensity score matching, 25 patients were included in each group. The SRATS group was associated with a lower conversion rate to multi-port surgery (0% vs. 20%, p = 0.05), shorter chest tube drainage duration (1.32 ± 0.75 vs. 2.00 ± 1.29 days, p = 0.003), and a shorter postoperative hospital stay (2.52 ± 1.00 vs. 5.08 ± 5.20 days, p = 0.003). Subxiphoid SRATS thymectomy using the SPS is feasible and is a good alternative to conventional thymectomy. Further studies are necessary to confirm its benefits.