The objective of this study was to describe the clinical characteristics, outcome and factors that may affect the outcome of childhood-onset myasthenia gravis (CMG) patients in China. We have followed up 424 patients with CMG for at least 5 years at Tongji Hospital. At the end of follow-up, the outcome of all the patients was measured according to MGFA Post-intervention Status. In this study, the patients have been followed up for 9.8 +/- A 5.4 years. The mean onset age was 5.4 +/- A 3.6 years. Ocular myasthenia gravis (OMG) was the major type of CMG within 2 years after onset (95 %). Thymic hyperplasia was found in 116 patients, and thymoma was confirmed in 6 patients. Acetylcholine receptor antibodies were elevated in 69.5 % of the patients. All the patients were routinely treated. Thymectomy was performed in 34 patients (8.0 %). At the end of follow-up, seventy-one patients (16.7 %) were significantly improved, 66 patients (15.6 %) remained unchanged, 53 patients (12.5 %) were worsened, and 234 patients (55.2 %) were exacerbated. Importantly, fifty OMG patients (12.4 %) had transformed into generalized myasthenia gravis (GMG) over 2 years after onset. Thymectomy did not effectively reduce the transformation from OMG to GMG. However, GMG cases significantly benefited from the surgery. This study indicated that the cases with autoimmune CMG account for over 50 % in Chinese MG population. The long-term follow-up discloses that CMG patients have a low percentage of improvement, and a high percentage of worsening and exacerbation. The treatment should not be withdrawn too early after the patients obtain complete stable remission. More studies are needed to gain better control of CMG symptoms.