Background: Studies exploring interventions targeting the cervical spine to improve symptoms in patients with temporomandibular disorders (TMD) are limited. Objectives: To determine whether mobilisation of the upper cervical region and craniocervical flexor training decreased orofacial pain, increased mandibular function and pressure pain thresholds (PPTs) of the masticatory muscles and decreased headache impact in women with TMD when compared to no intervention. Methods: In a single‐blind randomised controlled trial, 61 women with TMD were randomised into an intervention group (IG) and a control group (CG). The IG received upper cervical mobilisations and neck motor control and stabilisation exercises for 5 weeks. The CG received no treatment. Outcomes were collected by a blind rater at baseline and 5‐week follow‐up. Orofacial pain intensity was collected once a week. A mixed ANOVA and Cohen's d were used to determine differences within/between groups and effect sizes. Results: Pain intensity showed significant time‐by‐group interaction (P < 0.05), with significant between‐group differences at four and five weeks (P < 0.05), with large effect sizes (d > 0.8). The decrease in orofacial pain over time was clinically relevant only in the IG. Change in headache impact was significantly different between groups, and the IG showed a clinically relevant decrease after the treatment. No effects were found for PPT or mandibular function. Conclusion: Women with TMD reported a significant decrease in orofacial pain and headache impact after 5 weeks of treatment aimed at the upper cervical spine compared to a CG.