Haemophilus influenzae was the main causative organism for acute epiglottitis in the pre-Haemophilus influenzae type b (Hib) vaccine era. However, with current widespread Hib vaccination, the causative organisms may have changed. Here, we report the case of a healthy infant with acute epiglottitis caused by community-acquired methicillin-resistant Staphylococcus aureus (MRSA). The patient was a healthy 17-day-old male infant without a family history of immunodeficiency syndrome. He had not been started on any vaccines. On the third day of illness, he was diagnosed with acute pharyngitis with exudation on the back of the larynx. Although treatment using cefotaxime was initiated, he showed stridor, difficulty in pronunciation, and cyanosis upon crying on the fourth day. On the fifth day, he was diagnosed with acute epiglottitis by laryngoscopy, which showed a downward spread of the exudation and laryngeal edema. He was intubated and started on artificial respiration. Due to the detection of MRSA from a pharyngeal swab culture, he was treated with vancomycin. His fever disappeared on the first day after admission, and he was extubated on the eighth day after admission. MRSA genome analysis of the patient sample revealed negative Panton-Valentine leukocidin, positive toxic shock syndrome toxin 1, and type IV clone of staphylococcal cassette chromosome mec. This is a first case of acute epiglottitis caused by MRSA with a Panton-Valentine leukocidin-negative and toxic shock syndrome toxin 1-positive staphylococcal cassette chromosome mec type IV clone, which is known as a community-acquired MRSA in Japan. Community-acquired MRSA may be considered a causative organism for acute epiglottitis in the post-Hib vaccine era.