Basilar artery occlusion (BAO) is an infrequent form of acute life-threatening stroke and may occur secondary to vertebral artery dissection (VAD). VAD, which occurs spontaneously and sometimes results from mechanical stress or blunt force trauma to the neck, sometimes occurs in the V1-V2 junction, but there are not many reported cases of those. Herein, we report a pictorially illustrative and clinically informative case of VAD in the V1-V2 junction following BAO. The patient was a 27-year-old woman who was transferred to our hospital with abrupt severe unconsciousness. On admission, she presented with generalized convulsions and respiratory arrest, and pan-scan CT and CTA indicated BAO. We performed mechanical thrombectomy and achieved recanalization of the basilar artery, and she was diagnosed with BAO secondary to the right VAD at the entry of the C6 transverse foramen (V1-V2 junction). In hindsight, she had scapula and back pain before the onset. She recovered with a modified Rankin scale score of 3 after 90 days from the onset. VAD sometimes occurs at its entry into the transverse foramen of the C6 vertebra. In this case, VAD may be affected by minor trauma and potentially histological fragility due to the embryonic development process. Although BAO is sometimes difficult to diagnose because it presents with various symptoms, BAO secondary to VAD should be considered in cases of abrupt severe unconsciousness preceded by neck, scapula, or back pain in young and healthy persons.