Background: Although headache is common in pediatrics, data for the Flemish population are missing. We explored headache-prevalence, and its association with communication-technology (CT) and physical activity (PA) in Flemish children and adolescents. Methods: A cross-sectional exploratory school-based questionnaire study was designed. Flemish boys and girls (5–18 years) completed a symptom-questionnaire. Primary outcomes: sociodemographic background, headache-prevalence, headache-characteristics, CT-use and PA characteristics (self-report). Secondary outcomes: associations between headache-characteristics, age, gender, and CT-use and PA-characteristics. Results: Four hundred twenty-four questionnaires were analysed: 5–7-years: n = 58; 8–11-years: n = 84; 12–15-years: n = 137; 16–18-years: n = 145. Fifty-five percent suffered from headache. Prevalence increased with age. More 16–18-year girls versus boys had headache. CT-use was the main headache-provocateur. Headache prevalence was significantly higher in a frequently physical active population. Conclusion: Our results suggest presence of headache in Flemish children and adolescents. PA-level associates with headache prevalence. However, children and adolescents with headache did not report more CT-use compared to controls.