[Purpose] Cervicogenic headache is a major problem in patients with upper cervical dysfunction. However, its physical therapy management is a topic of debate. This study aims to determine the effect of C1-C2 Mulligan sustained natural apophyseal glide mobilizations on cervicogenic headache and associated dizziness. [Participants and Methods] This study included 48 patients with cervicogenic headache, who were randomly assigned to three equal groups: Group A (Headache SNAG), group B (C1-C2 SNAG rotation), and group C (combined). Neck Disability Index was used to examine neck pain intensity and cervicogenic headache symptoms. The 6-item Headache Impact Test scale was used to examine headache severity and its adverse effects on social life and functions. Flexion-Rotation Test was used to assess rotation range of motion at the level of C1-C2 and confirmed by a cervical range of motion device. Dizziness Handicap Inventory scale was used to evaluate dizziness. The evaluation was done pre- and post-treatment and compared between the groups. [Results] Group C showed significant improvement in all variables compared with groups A and B. [Conclusion] Sustained natural apophyseal glide mobilizations used in the study were effective in reducing cervicogenic headache and dizziness in all groups with a greater improvement in the combined group. The use of cervical SNAG mobilizations is encouraged as a noninvasive intervention depending on the therapist’s assessment, findings, and clinical reasoning.