Central neuropathic pain (CNP) after stroke has not been studied in sufficient detail and published studies have only included patients with cerebral artery infarct or hemorrhage. This study evaluates the prevalence and factors associated with CNP after cerebral venous (and sinus) thrombosis (CVT). This observational study included all patients admitted to our stroke unit for CVT between January 2002 and December 2007. Clinical data for each patient were collected prospectively and were combined with retrospective review of neuroradiological imaging. CVT patients were systematically examined at the outpatient clinic at 6 months, 12 months, and annually thereafter, and information on long-term functional outcome, including the presence of CNP, were obtained by open-ended questions. A standardized CNP assessment was performed during the last outpatient visit and was based on the patient's interview and clinical examination. Pain characteristics were assessed by the DN4-questionnaire. CNP was considered when the patient met the following criteria: painful area within the area of sensory abnormalities and follow-up MRI showing brain parenchymal lesion. Among the 43 patients admitted for CVT, seven (16%) developed CNP during the first year of follow-up. Standardized CNP assessment was performed 24.9 ± 11.6 months after CVT: eight patients (19%) suffered from CNP. Initial motor deficit (87 vs. 17%, p < 0.001), initial sensory deficit (62 vs. 20%, p = 0.03), cerebral infarction (75 vs. 23%, p = 0.009), right-sided lesion on initial MRI (62 vs. 17%, p = 0.017), thalamic (37 vs. 0%, p = 0.005) and basal ganglia involvement (25 vs. 0%, p = 0.03) and vein of Galen occlusion (25 vs. 0%) were significantly associated with CNP. Despite several methodological limitations, CNP after CVT seems to be frequent, accounting for one-fifth of all cases of CVT. Some clinical and radiological factors might contribute to the development of CNP.