The aim of the present study was to assess the relationship between temporomandibular joint disorder (TMJD) and headache in children and adolescents. A prospective cross-sectional cohort study was carried out involving 93 children and adolescents (6 to 14 years of age) at the outpatient service of a dental school. All participants underwent a clinical examination involving Axis 1 of the Research Diagnostic Criteria for Temporomandibular Disorders, along with a characterization of headache and an anthropometric evaluation. Statistical analysis involved the chi-squared test for quantitative variables and the Student's t-test, ANOVA and Tukey's test for quantitative data. An adjusted logistic regression model was used to determine significant associations among gender, age, TMJD and headache. Mild TMJD was identified in 35.8% of the sample and was not associated the presence of headache. Moderate TMJD was found in 25.8% of patients and severe TMJD was found in 11.8%; both forms of TMJD were associated with headache. A significant correlation was found between the intensity of TMJD and the risk of headache. The present findings demonstrate a positive correlation between TMJD and headache in children and adolescents, independently of gender and age.