This population-based cross-sectional study examined the 3-month prevalence of headache, migraine and tension-type headache (TTH) among adolescents aged 12–15 years in Germany. Students (n = 3324) from 20 schools completed a questionnaire on general and headache-specific pain which included a sociodemographic module. The headache-specific questionnaire complied with the respective revised criteria of the International Headache Society (IHS). ‘Modified criteria’ changed the item ‘duration’ in migraine (>30 min instead of > 4 h). The overall 3-month prevalence of headache was 69.4% (boys 59.5%, girls 78.9%), with 4.4% of the adolescents suffering from frequent (≥14 days/3 months) and severe (grade 8–10 on a 10-point visual analogue scale) headache and 1.4% (boys 0.9%, girls 1.9%) from headache ≥ 15 days/month. The 3-month prevalence of migraine was 2.6% (boys 1.6%, girls 3.5%) applying strict IHS criteria and 6.9% (boys 4.4%, girls 9.3%) with modified criteria; 12.6% (boys 8.3%, girls 16.7%) suffered from probable migraine, 0.07% fulfilled the criteria for chronic migraine, 4.5% (boys 4.6%, girls 4.3%) suffered from TTH, 0.2% from chronic TTH and 15.7% (boys 14.5%, girls 16.9%) from probable TTH. Headache and migraine were more common in girls than in boys and in teenagers, especially in girls, aiming at higher education. Recurrent headache and primary headache disorders are common complaints among German adolescents, especially among girls.