Headache after cerebral venous thrombosis (post-CVT headache PCH) is a common complaint during follow-up. Risk factors and their pathophysiology are not well known. We studied PCH prevalence in CVT patients, its pathophysiology, and possible risk factors. We performed a retrospective observational study of patients admitted to a tertiary hospital between 2006 and 2019 with CVT and at least one follow-up appointment. We diagnosed PCH when patients reported headaches during the follow-up visit. Recanalization was retrospectively assessed by two neuroradiologists using the first available follow-up MRI/ MRV, and the PRIORITy-CVT study classification. Of 131 patients, sixty (60/131, 45.8 %) reported PCH at the 3-month follow-up. Of these PCH, 9 had previous migraine (9/60, 5.0 %) and 13 previous tension-type headaches (13/60, 21.6 %), before CVT. Forty-four (44/60, 73.3 %) PCH patients had de novo headache: 21 (21/60, 35.0 %) de novo tension-type headaches; 6 (6/60, 10.0 %) de novo migraine; 6 (6/60, 10.0 %) secondary headache disorders: 3 due to dural arteriovenous fistula, 2 due to intracranial hypertension, and 1 recurrent CVT, and 11 other headache types. Most patients had at least partial recanalization, with no difference in PCH frequency amongst recanalization subgroups (p = 0.598). Premorbid depression (p = 0.009, OR 7.9, 95 % CI 1.6-31.4) increased the odds ratio of PCH, while superior sagittal sinus thrombosis (p = 0.005, OR 0.15, 95 % CI 0.03-0.56) decreased it. Our study shows that PCH is a common finding after CVT and elucidates potential risk factors. PCH is common in patients with previous or de novo primary headache. In PCH patients without previous headache, secondary causes of headache, namely related to CVT complications, should be excluded. PCH is also increased in patients with premorbid depression. There was no statistically significant difference in PCH amongst the PRIORITy-CVT recanalization subgroups, but most patients had at least partial recanalization.