A recent evidence-based review failed to show conclusive benefits of thymectomy in non-thymomatous MG patients, and only recommended thymectomy as an option to increase the probability of remission or improvement. Furthermore, it is a matter of another controversy whether thymectomy is beneficial in ocular MG and also late-onset MG patients without thymoma. We reviewed the clinical course and outcomes of ocular MG and late-onset MG patients in a retrospective cross-sectional multi-center survey conducted in Japan. Our data shows that thymectomy may prevent, or limit the severity of, the generalization of the disease but do not improve ocular symptoms. For late-onset MG, thymectomy is a potentially effective treatment. Another problem is that postoperative course can fluctuate and sometimes postoperative respiratory failure and myasthenic crisis may occur. We described that perioperative steroid therapy is feasible and have clinical benefits for generalized MG with fluctuating symptoms. Mainly after thymectomy, tacrolimus or cyclosporine therapy may allow steroid daily doses to be reduced in MG patients who intended to reduce concomitant steroid use.