Background Disability imposed by headache disorders constitutes an expressive economic burden, mostly from indirect costs due to absenteeism and presenteeism. Objective To estimate indirect costs from absenteeism and presenteeism due to headache disorders in Brazil. Methods In a secondary, descriptive analysis of two nationwide databases, we estimated indirect costs based on headache-related disability and socioeconomic data. Results In the first database analyzed (n = 3838), 12.8% of the employed population with headache disorders missed at least 1 day of work in the last 3 months (mean, 95% CI = 4.2 days [3.7–4.6]). Based on the prevalence of headache disorders, days lost due to headaches and income data, R$ 40.4 billion (Int$ 20 billion) are lost due to headache-related absenteeism annually. For presenteeism, 26.2% of the employed population with headache disorders worked at least 1 day in the last 3 months with 50% reduced productivity (mean, 95% CI = 5.7 days [5.3–6.2]), amounting to R$ 27.3 billion (Int$ 13.5 billion) of financial loss annually. In the other database analysed (n = 205,546), 14,052 (6.8%) respondents missed work/school or household duties in the past 2 weeks due to some disease. Of these, 4.7% attributed their days lost to headaches disorders in the economically active population, which ranked 4th as main cause of days lost due to disease, among 23 common diseases. Conclusions The economic burden of headache disorders in Brazil, mostly due to migraine (55.4%), may cost up to R$ 67.6 billion (Int$ 33.5 billion) annually, and headache disorders represent a leading cause of absenteeism due to disease.