Sexually transmitted diseases (STDs) are causes of public health burden globally. The purpose of this study is to document age-specific and sex-related changes in the morbidity of four representative STDs in children. Japanese national surveillance data from 1999 to 2017 on morbidities of the following four STDs were analyzed by age and sex: Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), condylomata acuminate (CA), and genital herpes simplex virus (GHSV). The morbidities of males and females in each age group were compared through the male-to-female morbidity (MFM) ratios. The MFM ratios were not different from one in infants, less than one in children, and greater than one after puberty in all four STDs. The reversal of MFM ratio less than 1 to greater than 1 for NG infection was observed between 10–14 and 15–19 year of age, i.e., during the puberty, while that for GHSV infection was observed between 35–39 and 40–44 year of age, i.e., during adulthood. In conclusion, the morbidities of the four STDs were similar between the sexes in infants, and were higher in female children than in male children, while the morbidities in all four diseases were higher in men after puberty.