Dysmenorrhea is a common menstrual disorder experienced by adolescents, and its major symptoms, including pain, adversely affect daily life and school performance. However, little epidemiologic evidence on dysmenorrhea in Japanese adolescents exists. This cross-sectional study aimed to determine the prevalence of and identify factors associated with dysmenorrhea in Japanese female junior high school students. Among 1,167 girls aged between 12 and 15 years, 1,018 participants completed a questionnaire that solicited information on age at menarche, menstruation, and lifestyle, as well as demographic characteristics. Dysmenorrhea was defined based on menstrual pain using a Visual Analog Scale (VAS), with moderate or severe (moderate-severe) dysmenorrhea, which adversely affects daily life, defined as VAS ≥ 4, and severe dysmenorrhea defined as VAS ≥ 7. The prevalence of moderate-severe dysmenorrhea was 476/1,018 (46.8%), and that of severe dysmenorrhea was 180/1,018 (17.7%). Higher chronological and gynecological ages (years after menarche) were significantly associated with a higher prevalence of dysmenorrhea regardless of severity (P for trend < 0.001). In addition, short sleeping hours (< 6/day) were associated with moderate-severe dysmenorrhea (OR = 3.05, 95%CI: 1.06-8.77), and sports activity levels were associated with severe dysmenorrhea (P for trend = 0.045). Our findings suggest that dysmenorrhea that adversely affects daily activities is highly prevalent, and may be associated with certain lifestyle factors in junior high school students. Health education teachers should be made aware of these facts, and appropriately care for those suffering from dysmenorrhea symptoms, absentees, and those experiencing difficulties in school life due to dysmenorrhea symptoms.