This single-center retrospective exploratory analysis evaluated the effects of sugammadex compared with neostigmine on postoperative recovery in patients with myasthenia gravis (MG) who underwent video-assisted thoracoscopic surgery (VATS)–thymectomy. This retrospective study included 180 patients with MG, aged >18 years, who received sugammadex (sugammadex group, n = 83) or neostigmine–glycopyrrolate (neostigmine group, n = 88) after VATS–thymectomy between November 2007 and December 2020. Inverse probability of treatment weighting (IPTW) adjustment was performed to balance the baseline characteristics between the two groups. The primary outcome was the length of postoperative hospital stay, and the secondary outcomes were the incidence of postoperative mortality and complications, as well as the postoperative extubation and reintubation rates, in the operating room after VATS–thymectomy; the outcomes were compared between the two groups. After IPTW adjustment, the sugammadex group showed a significantly shorter median postoperative hospital stay than the neostigmine group (4 (2, 4) vs. 5 (3, 6) days, respectively; p = 0.003). There were no significant differences between the two groups in the incidences of postoperative complications (including postoperative myasthenic crisis, nerve palsy, atelectasis, and pleural effusion). Patients with MG following VATS–thymectomy who received sugammadex showed a significantly shorter postoperative hospital stay than those who received neostigmine.