The most accepted mechanism of cervicogenic headache is referred pain from cervical structures innervated by the upper three cervical spinal nerves. The lateral atlantoaxial joint is not an uncommon cause of cervicogenic headache. In this retrospective study, we examined the effect of lateral atlantoaxial intra-articular steroid injection in managing 32 patients with cervicogenic headache who have a clinical picture suggestive of atlantoaxial joint pain. The data were collected retrospectively by reviewing the patient's medical records and pain questionnaires. A total of 115 patients with cervicogenic headache who were referred to our institute were identified. Of those patients, 32 had a clinical picture suggestive of atlantoaxial joint pain and subsequently underwent a diagnostic/therapeutic intra-articular block. Fifteen of the 32 patients (46.8%) had a postprocedure pain score of 0 (95% CI = 17.5-72.1%). Twenty-six of the 32 patients (81.2%) had a decrease in their postprocedure pain score of 50% or more (95% CI = 62.4-97.6%). The mean preprocedure pain score was 6.8 and postprocedure was 2.2 (Bonferroni-adjusted P < 0.001). At 1 and 3 months, the mean pain scores were 1.9 (P < 0.001) and 3.6 (P < 0.008), respectively. However, at 6 months, the mean pain score was 3.7, and this was not statistically significant (P = 0.208). Lateral atlantoaxial intra-articular corticosteroid injections may provide short-term analgesia for patients with pain originating from the lateral atlantoaxial joint.