We compared the lifetime prevalence and the prevalence of headache during the previous year in patients with Parkinson's disease (PD) and control subjects. We also investigated the association between the side of PD symptom onset and the side of the headache. We interviewed 98 consecutive patients with an established diagnosis of PD between December 2010 and January 2012. The control group consisted of the 98 oldest sex-matched individuals from the nationwide Brazilian headache database. PD patients showed a significantly lower prevalence (40.8%) of headache in the previous year than controls (69.4%) (adjusted OR 0.5, CI 95% 0.2-0.9, p = 0.03). PD patients also showed a lower prevalence of headache throughout life (74.5%) than controls (93.9%) (adjusted OR 0.2, CI 95% 0.1-0.6, p = 0.01). Considering only patients who presented headache during the previous year, PD patients showed a higher association with occurrence of migraine than tension-type headache compared with controls (adjusted OR 3.3, CI 95% 1.2-8.9, p = 0.02). The headache side was ipsilateral to the side of PD onset in 21 patients (84%), with a concordance of 85.7% on the left side and 81.8% on the right side (p < 0.01). The prevalence of primary headache was significantly lower in patients with PD than controls. The predominant side of headache was ipsilateral to the side of initial motor signs of PD.