Objective Limited evidence has led to ongoing debate about the benefits of thymectomy for late‐onset myasthenia gravis (LOMG). This study aims to compare the outcomes of patients with LOMG who underwent thymectomy versus those who received medical treatment alone, and evaluate the incidence of surgical adverse events. Methods Non‐thymomatous acetylcholine‐receptor antibody positive patients with LOMG were selected from a multi‐center longitudinal clinical database. Rates of and time to response (remission and minimal manifestations status) were compared between 2 groups by propensity score matching (PSM), Kaplan–Meier analysis, and Cox regression models. Additionally, the incidence of adverse events about thymectomy was compared between LOMG and younger patients with myasthenia gravis (MG) aged 40 to 50 years old. Results A total of 55 and 210 patients with LOMG were enrolled in the thymectomy and medical treatment groups, respectively. The thymectomy group exhibited significantly younger onset age (56.31 ± 6.15 vs. 62.04 ± 7.83, p < 0.001). After PSM adjustment, thymectomy demonstrated a greater cumulative probability ( p < 0.001), and the 2.356‐fold (95% confidence interval [CI] = 1.537–3.612, p < 0.001) higher chance of better outcomes compared to medical treatment. In subgroup analysis, thymectomy showed significantly higher response rates compared to medical treatment alone at 24 ± 2 months (48.9%, 95% CI = 33.7–64.1% vs 23.8%, 95% CI = 14.2–33.3%, p = 0.004), and 36 ± 2 months (59.5%, 95% CI = 42.9–76.1% vs 28.9%, 95% CI = 18.5–39.4%, p = 0.002). The incidences of adverse events were comparable between patients with LOMG and younger patients with MG (32.0% vs 22.4%, p = 0.286). Interpretation Thymectomy may be an effective therapeutic option for LOMG. Our findings highlight the need for further development of a randomized trial targeting patients with LOMG. ANN NEUROL 2025