Purpose: This report presents a case of repeated toxic conjunctival necrosis caused by amikacin eye drops in a patient with a corneal ulcer induced by Mycobacterium abscessus (M. abscessus).Case summary: During treatment for herpetic keratitis with complaints of conjunctival hyperemia and eye pain in the right eye for 1 month. Slit-lamp microscopy revealed a circular corneal epithelial defect and stromal infiltration of her right eye. Gram staining and culture were performed, and eye drops were prescribed for empirical treatment. The bacterial culture grew M. abscessus. Antibiotic susceptibility tests showed resistance to quinolone. The patient was prescribed amikacin eye drops and the corneal epithelial defects improved. Two weeks later, circular conjunctival epithelial defects and hyperemia were observed on the inferior conjunctiva. Conjunctival necrosis caused by amikacin was suspected. The amikacin eye drops were discontinued and the conjunctival lesion improved. However, the patient’s corneal ulcer recurred. The amikacin eye drops were restarted, but conjunctival toxicity recurred, so she was treated with topical clarithromycin and moxifloxacin. The eye drops were gradually reduced and the lesion healed leaving mild corneal opacity.Conclusions: M. abscessus-induced keratitis resistant to quinolone antibiotics requires long-term combined therapy with multiple drugs. Amikacin eye drops should be used carefully as conjunctival toxicity may occur.