The pathophysiology of primary exertional headache (EH) is unknown. Physical exertion is associated with Valsalva-like manoeuvres (VM). VM leads to increased intrathoracic pressure and reduces cerebral venous drainage. Internal jugular vein valve incompetence (IJVVI) leads to retrograde venous flow during VM with transient increase of intracranial pressure. We analysed the prevalence of IJVVI in EH patients using duplex ultrasound. Bilateral measurements were performed at rest and during VM in 20 patients and 40 controls. Incompetence was concluded if retrograde venous flow could be seen in the jugular Doppler spectrum during repeated VM. Seventy percent of EH patients and 20% of controls demonstrated IJVVI, yielding a significant difference (P = 0.0004). IJVVI was always observed on the dominant venous drainage side. Our study suggests that intracranial venous congestion caused by retrograde jugular venous flow might play a role in the pathophysiology of EH with IJVVI as a risk factor.