A 23-year-old woman with binocular vertical diplopia, bilateral ptosis (which worsened with left and down gazing), dysarthria, and dysphagia visited the outpatient department. She had received a primary HPV nine-valent vaccination 2 months prior and a second vaccination 5 days before the visit. The symptoms occurred on the 3rd day after the second vaccination. The muscular strength of her upper and lower extremities was normal, and the deep tendon reflex of both sides was normal. Her ptosis and diplopia temporarily improved with an ice pack and pyridostigmine test. The repetitive nerve stimulation (RNS) did not reveal a significant decrement in deltoid, abductor digiti minimi, flexor carpi, and orbicularis oculi muscles. The serum AChR antibody titer was 1.66 nmol/L. Other autoimmune disease tests, including rheumatoid factor and antinuclear antibody, were negative. A thyroid function test was normal, and no thymus abnormality was observed on chest computed tomography (CT). She was diagnosed with MG, and pyridostigmine oral administration and high-dose intravenous steroid therapy were initiated. Her dyspnea became more severe on the 2nd day after admission, and oxygen saturation decreased; therefore, she received intravenous immunoglobulin therapy. Afterward, spontaneous breathing became more difficult, and the dysphagia and bilateral ptosis worsened. These symptoms were determined to demonstrate an MG crisis, and mechanical ventilation was initiated after endotracheal intubation. Although muscle strength was normal at admission, the extension power of the distal fingers decreased. On the 7th day after admission, sudden tachycardia was observed, the patient experienced persistent pressure in the right chest, and oxygen saturation decreased during mechanical ventilation. Chest CT revealed a low-density-filling defect of the pulmonary artery in the right lower lobe. Ischemic changes in the lung parenchyma and an increased D-dimer level (2199 ng/mL) were also observed. Therefore, heparin treatment was initiated owing to the possibility of pulmonary embolism. The D-dimer level decreased to within the normal range (99 ng/mL) in the 2nd week after the increase. In the 4th week of hospitalization, the symptoms further improved such that she could walk and the AChR antibody titer decreased (0.99 nmol/L). However, right eye ptosis and binocular vertical diplopia persisted. She was discharged after the dysphagia had completely resolved. The AchR antibody titer was normal (0.05 nmol/L) at discharge. The patient has returned to daily life without symptom recurrence or further treatment.