ObjectivesPatients with myasthenia gravis (MG) often benefit from thymectomy, but the optimal timing of extubation following thymectomy in these patients remains unknown. This study of MG patients compared the effect of early and late extubation following thymectomy on clinical outcome.MethodsWe performed a study of data from 96 patients with MG who received thymectomy procedures, followed by early (< 6 h) or late (> 6 h) extubation, at our institution between October 2011 and November 2017. Patient clinical and demographic characteristics, preoperative data, and postoperative clinical outcomes were analyzed. Data sharing is not applicable to this article as no datasets were generated or analyzed during the current study.ResultsThe patients in the early extubation group (n = 53) and late extubation group (n = 43) had similar preoperative clinical and demographic characteristics. However, the early extubation group had a significantly longer duration of MG (24 months vs. 12 months, P < 0.013) and a lower incidence of reintubation (11.3% vs. 37.2%, P = 0.003). Postoperative pulmonary infection was significantly more common in the late extubation group (39.5% vs. 11.3%, P = 0.001; adjusted odds ratio = 6.94, 95% CI 1.24–38.97). Also, patients in the late extubation group had a longer duration of ICU stay (6.4 ± 4.0 h vs. 4.3 ± 1.8 h; P = 0.003) and had a longer adjusted duration of ICU stay by 0.93 days (95% CI 0.02–1.85).ConclusionsOur analysis of patients with MG who received thymectomy procedures indicated that early extubation was associated with improved clinical outcomes, in particular with reduced risk of postoperative pulmonary infection and reduced ICU stay.Electronic supplementary materialThe online version of this article (10.1007/s10072-019-03941-0) contains supplementary material, which is available to authorized users.