Aims: This study aimed to characterize the clinical features of headache in patients with non-thrombotic internal jugular vein stenosis (IJVS) and to identify associated risk factors. Methods: This retrospective study consecutively enrolled patients with imaging-confirmed non-thrombotic IJVS from January 2021 through July 2024. Participants were divided into IJVS-headache and IJVS-without-headache groups based on clinical symptoms. Demographic, clinical, neuroimaging, and treatment data were reviewed in detail. Univariate and multivariate logistic regression analyses were performed to determine risk factors for headache. Results: Among 283 eligible patients (median age: 51 years in the IJVS-headache group vs. 56 years in the IJVS-without-headache group, p < 0.001), 65.02% reported headache. Most headaches were chronic (82.07%), generalized (85.87%), and moderate in intensity (53.26%), with notable daily life impact (57.61%). Univariate analysis showed that headache was significantly associated with visual disturbances (p = 0.010), elevated cerebrospinal fluid opening pressure (p < 0.001), high jugular bulb (p = 0.007), and severe scalp vein dilation (p < 0.001), but inversely associated with severe vertebral vein expansion (p < 0.001). Multivariate regression revealed that high jugular bulb (OR = 3.144, 95% CI: 1.083-9.123, p = 0.035), severe scalp vein dilation (OR = 2.142, 95% CI: 1.068-4.294, p = 0.032), and protein C or S deficiency (OR = 5.984, 95% CI: 1.196-29.928, p = 0.029) were independent risk factors, whereas severe vertebral vein expansion was protective (OR = 0.184, 95% CI: 0.092-0.366, p < 0.001). Conclusions: Headache represents a prevalent and often disabling symptom in non-thrombotic IJVS, underpinned by distinctive vascular and hematologic profiles. Identification of high-risk patients based on neuroimaging and thrombophilia screening may facilitate personalized interventions and improve symptom control.