Background Although voriconazole is a widely used azole antifungal agent in clinical practice, its side effect of muscle toxicity is extremely rare. The present study demonstrates an adverse effect of progressive myotoxicity induced by intravenous voriconazole in a cryptogenic organizing pneumonia patient misdiagnosed as suspected pulmonary fungal infection.Case presentation A 78-year-old male was admitted to our hospital due to recurrent cough and expectoration for four months. His previous chest CT scan indicated alveolar opacities and multiple cavitary nodules in the right lower lobe. Pulmonary fungal infection was considered due to weakly positive results of serum galactomannan and 1,3 β-D-glucan test,with no evidence of malignant tumor, tuberculosis, or Wegener's granulomatosis. The patient experienced diffuse myalgia with significantly elevated muscle enzymes after voriconazole administration for 13 days, and recovered uneventfully due to immediate voriconazole cessation and enhanced intravenous fluid infusion. Furthermore, the pulmonary cavitary nodules were consistent with the pathological findings of cryptogenic organizing pneumonia.Conclusions Voriconazole-associated myotoxicity should be considered when a patient presents with evidence of muscle injury during voriconazole administration. Morever, although invasive pulmonary fungal infection can often show multiple nodules with cavities in CT scan, the initiation of anti-fungal agents should be cautious before the pathological features of multiple cavitary nodules are identified, in order to avoid potential serious adverse events.