Background Mycoplasma pneumonia (M. pneumoniae) is one of the key pathogens of community-acquired pneumonia. A global pandemic of M. pneumoniae has occurred since 2010. The aim of this study was to survey the prevalence of M. pneumoniae in children in Beijing from 2007-2012. Methods A total of 3 073 clinical specimens were obtained from pediatric patients with respiratory tract infections from January 2007 to December 2012, and examined by nested polymerase chain reaction. PCR products were visualized by 2% agarose gel electrophoresis, positive products sequenced, and compared with reference sequences in GenBank. Macrolide resistance-associated mutations were also detected for some positive samples. Results Of the 3 073 specimens, 588 (19.13%) were positive for M. pneumoniae, 12.4% of which were accompanied by viral infections. Positive rates for M. pneumoniae were highest in 2007 and 2012, showing a signifcant difference when compared with other years. Infections tended to occur in autumn and winter and positive rates were signifcantly higher for children aged 3-16. The rate of macrolide resistance-associated mutations was 90.7%, and the predominant mutation was an A→G transition (89.92%) at position 2063 in domain V of the 23S rRNA gene. Conclusions M. pneumoniae outbreaks occurred in 2007 and 2012 in pediatric patients in Beijing, which is consistent with the global prevalence of M. pneumoniae. M. pneumoniae can cause multi-system infections in children, and may be accompanied with viral infections. We determined that school-age children are more susceptible to this disease, particularly in autumn and winter. Gene mutations associated with macrolide resistance were very common in M. pneumoniae-positive specimens during this period in Beijing.