Background: We detected a community outbreak of macrolide-resistant Mycoplasma pneumoniae infection that occurred predominantly among students at 2 schools in Yamagata, Japan. Methods: Throat swab specimens were collected from patients who were clinically suspected to have M. pneumoniae infection after testing negative for influenza virus by a nasopharyngeal swab rapid antigen test. We performed cultures for M. pneumoniae, and all isolates were sequenced for the presence of a mutation of the 23S rRNA gene. Results: Of 96 specimens collected between July 2009 and January 2010, 83 were from students attending junior high school A and primary schools B, C and D. A total of 47 M. pneumoniae isolates were obtained; among them, 25, 15 and 4 were isolated from students attending schools A, B and D, respectively, and M. pneumoniae could not be isolated from students who attended school C. An A2063T mutation in domain V of the 23S rRNA gene, which is associated with macrolide resistance, was identified in 39 (83.0%) isolates. The rates of macrolide resistance at schools A, B and D were 96.0%, 86.7% and 0%, respectively. The minimum inhibitory concentrations for isolates with an A2063T transversion showed high resistance to clarithromycin (minimum inhibitory concentration, 16-64 mg/L), and clarithromycin prescribed initially was clinically ineffective. Conclusions: This school-based cluster of macrolide-resistant M. pneumoniae infections, which was identified in 2 geographically close schools, indicates that the transmission principally occurred by close contact between students at school. Monitoring the spread of macrolide-resistant M. pneumoniae and clinical guidelines for the appropriate medication against such infections would be needed to control outbreaks of M. pneumoniae.