Ehlers–Danlos syndrome (EDS) type IV is characterized by thin skin with visible veins, easy bruising, characteristic facial features, arterial and digestive complications, as well as rupture of the gravid uterus. It has never been previously reported that trigeminal autonomic cephalalgias (TACs) could manifest as the only initial symptom of EDS type IV. Here, we report a case of a 27-year-old man who presented atypical headache like TACs stimulated by right internal carotid artery dissection. About one month after his discharge, he suffered dissection of the right renal artery and splenic artery, in addition to partial infarction of the right kidney and spleen. Genetic testing revealed a novel splicing variant c.799-1G>A within COL3A1. He was ultimately diagnosed with Ehlers–Danlos syndrome type IV. This case expanded the genetic spectrum and clinical manifestation of EDS type IV and provided a significant implication for the diagnosis of EDS type IV when the initial symptom manifested as TACs, not the typical presentation of EDS type IV.