A cervicogenic headache (CEH) is difficult to diagnose due to its varied pathology. We evaluated the usefulness of single-photon emission computed tomography/computed tomography (SPECT/CT) in diagnosing CEH and its interventional treatment. Retrospectively, 23 patients diagnosed with CEH between March 2016 to August 2018 were allocated to SPECT/CT ( = 11) and control ( = 12) groups. The SPECT/CT group was further stratified into SPECT/CT(+) and SPECT/CT(-) groups according to the presence of positive findings. Patients in the SPECT/CT group underwent an intra-articular injection at a radiologically verified lesion site, whereas those in the control group underwent third occipital nerve block. Clinical outcomes were evaluated with the visual analog scale (VAS), neck disability index (NDI), and global perceived effect (GPE) scale at baseline, and at one, three, and six months postoperatively. The SPECT/CT group showed less VAS, NDI, and GPE scores at six months postoperatively (2.91 ± 2.30 vs. 4.42 ± 1.62, = 0.08; 38.00 ± 16.54 vs. 48.7 ± 12.40, = 0.093; 2.00 ± 1.41 vs. 3.17 ± 1.11, = 0.039). Successful responders at six months postoperatively were higher in the SPECT/CT(+) group than in the control group (75% vs. 0%). SPECT/CT can identify arthritic changes and accurately define therapeutic targets.