OBJECTIVE: Cervicogenic headache affects a significant portion of the entire population. This type of headache especially with atypical presentation is often hard to diagnose and manage since its etiopathophysiology is not been yet well understood. We have investigated the prevalence of cervicogenic headache with atypical presentation and discussed the etiology of it, and the outcome of surgical intervention on this type of headache in patients with cervical degenerative disease. PATIENTS AND METHODS: Radiological and clinical data of 160 patients (from 2001 through 2016) were retrospectively reviewed. Significant differences between the groups were determined by chi-square test. Logistic regression analysis was performed to identify the predictors of unfavorable outcome. RESULTS: In this study, 10% of the patients had atypical presentation of cervicogenic headache. In overall cohort, after surgical intervention, there was significant improvement in symptoms and pain control, whether the presentation is typical or atypical. Sixty-one percent of the patients had no complaints, and 90% of the patients were headache-free (p<0.0001). Sixty-nine percent of the patients were free of neck, shoulder and extremity pain, and visual analogue scale pain score was reduced by 7 points (pre-op, 8.4 vs. last follow-up, 1.5, p<0.0001). However, number of patients with reduced headache was significantly higher in the group with typical presentation of headache (90.1%) compared to group with atypical (80%) presentation, p=0.04. In this study, female gender, smoking, obesity and depression were identified as predictors of overall unfavourable outcome. In addition, in a separate analysis, smoking and depression were revealed as risk factors for persistent headache. CONCLUSIONS: A notable portion of patients with cervicogenic headache can have an atypical presentation mimicking a primary type headache. However, cervicogenic headaches with atypical presentation can be difficult to diagnose and manage at the initial visit of the patients. Etiopathophysiology of this type of headache could be explained by the theories including discogenic, convergence and sensitization-desensitization theories. When cervicogenic headache is accompanied with CDD, performing ACDF or laminectomy would be the treatment of choice. Surgical intervention can also relieve the accompanying neck, shoulder and extremity pain with minimal complications. Lastly, outcomes of surgical intervention depend on the patients' morbidities including obesity, smoking and depression.