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Although accurate targeting of the causative muscles is of paramount importance in the treatment of focal dystonia, this is often challenging due to distortion of the affected anatomical structures and difficulty in proper positioning of injections. We report a case of idiopathic cervical dystonia that was treated by CT-guided injection of botulinum toxin (BTX) into multiple deep muscles.Based on clinical presentation of combined torticollis and retrocollis, and needle electromyography (EMG) results, BTX was injected under EMG guidance. This treatment resulted in no improvement.Subsequently, target muscles were identified using fludeoxyglucose (18F-FDG) fusion positron emission tomography/computed tomography (18F-FDG PET/CT). BTX was injected into the hypermetabolic muscles. This injection successfully relieved the symptoms, and nine months of follow-up using PET/CT confirmed that hypermetabolic muscles had been normalized. This case indicated that CT guidance may facilitate accurate targeting of BTX injection. To the authors’ knowledge, this is the first case reporting a positive effect of BTX on cervical dystonia symptoms that lasted nine months, confirmed by follow-up PET/CT.