We experienced a case of neurological deterioration after decompressive suboccipital craniectomy (DSC) in a patient with a brainstem-compressing thrombosed giant aneurysm of the vertebral artery (VA). A 60-year-old male harboring a thrombosed giant aneurysm (about 4 cm) of the right vertebral artery presented with quadriparesis. We treated the aneurysm by endovascular coil trapping of the right VA and expected the aneurysm to shrink slowly. After 7 days, however, he suffered aggravated symptoms as his aneurysm increased in size due to internal thrombosis. The medulla compression was aggravated, and so we performed DSC with C1 laminectomy. After the third post-operative day, unfortunately, his neurologic symptoms were more aggravated than in the pre-DSC state. Despite of conservative treatment, neurological symptoms did not improve, and microsurgical aneurysmectomy was performed for the medulla decompression. Unfortunately, the post-operative recovery was not as good as anticipated. DSC should not be used to release the brainstem when treating a brainstem-compressing thrombosed giant aneurysm of the VA.