Background: Cervicogenic headache is a common condition causing significant disability. Recent studies have shown high incidence of Cervicogenic headache, which is evaluated by flexion-rotation test (FRT). To manage this dysfunction, C1-C2 self-Sustained Natural Apophyseal Glide (SNAG), deep cervical flexors strength training exercise and conventional exercises were used. Methods: A sample of 30 subjects (30±5 years) with cervicogenic headache were randomly allocated into C1-C2 self-SNAG and deep cervical flexors strength training group. After an initial instruction and practice visit in the clinic, interventions consisted of self-SNAG, deep cervical flexors strength training along with conventional treatment applied twice daily on a continual basis 5 days a week for 4 weeks. Pain intensity and head ache symptoms were measured by VAS and head ache disability index which is measured at baseline, 4th, 8thweek and 6th month. Results: Mann Whitney test shows no differences between groups at baseline values. After 4 weeks VAS decreased for the C1-C2 self-SNAG group (P‹0.05) compare with deep flexor training group. It was substantially less in C1-C2 self-SNAG group compare with deep cervical strength training group during 8th week and 6th month. There was also significant difference for the variable headache disability Index between group (P‹0.05) at 4 week, 8th week and 6th month. Conclusions: These results suggest that C1-C2 self-SNAG technique is effective in the management of individuals with cervicogenic headache than deep cervical flexors strength training exercise