Background and Objectives: Physiotherapy approaches are used to eliminate the problems caused by cervicogenic headache (CHA), known as secondary headache associated with the structures of the upper cervical region. This study aimed to investigate the effects of cervical mobilization (CM) with clinical Pilates exercises (CPE) on pain, muscle stiffness and head–neck blood flow in CGH. Materials and Methods: A total of 25 patients participated in this randomized controlled study and were randomized into either the CM group or the CM+CPE group. All treatment methods were applied 3 days a week for 6 weeks. The outcome measure was headache intensity and frequency, the number of analgesics, muscle stiffness and vertebral artery (VA) and internal carotid artery (ICA) blood flow. Headache intensity was measured by a visual analogue scale, muscle stiffness by a myotonometer and blood flow by Doppler US. Evaluations were repeated after 6 weeks of treatment. Within-group comparisons were made by the Wilcoxon signed rank test, and between-group comparisons were made by the Mann–Whitney U test. Results: After treatments in the two groups, headache intensity and frequency and the number of analgesics decreased, the muscle stiffness of the suboccipital, upper trapezius and sternocleidomastoid (SCM) muscles decreased, and the blood flow of the ICA and VA increased (p < 0.05). There was a significant difference between the groups in terms of headache intensity (p = 0.025) and muscle stiffness in SKM (p = 0.044) in favor of the CM+CPE group. Conclusions: Non-pharmacological treatment approaches have an important role in CHA related to the upper cervical region. This study suggests that it would be beneficial to add CM in combination with CPE to the non-pharmacological treatment of patients with CHA.