Herein, we report a case of otitis media caused by methicillin-resistant Staphylococcus aureus (MRSA), presenting as falsely positive for proteinase 3 (PR3)-antineutrophil cytoplasmic antibodies (ANCA). A 47-year-old woman was referred to our hospital with a complaint of left otorrhea. An otorrhea culture yielded MRSA, and the patient was treated using tympanoplasty. Postoperative administration of teicoplanin lead to drug-induced neutropenia and was discontinued 4 days after the operation. One month after the operation, the patient's otorrhea recurred, and it was accompanied by hearing impairment. The otorrhea culture yielded MRSA again, while serum was positive for PR3-ANCA (6.8 U/mL). As MRSA was detected in the patient's otorrhea sample, she was treated with linezolid. Her symptoms then improved immediately. Although the PR3-ANCA positivity remained, the patient's otorrhea and hearing impairment had not recurred for 3 years when this report was submitted. Therefore, we conclude that this is a case of false PR3-ANCA positivity.