(1) Background: There are links between tension-type headache and/or migraine with dysfunctions of the cervical and masticatory muscles and with psychosocial factors. The study aims to highlight the connections between primary headaches, bruxism and psychosocial issues, the effectiveness of a multidisciplinary approach in decreasing the intensity and frequency of the headache episodes and bruxism. (2) Methods: 67 patients with primary headache and bruxism were divided into two equal groups. The subjects attended manual therapy sessions twice a week and a weekly counselling session for three months. (3) Results: an overall comparison before and after three months show a significant decrease of the qualitative variables (tension-type headache, migraine, awake bruxism, limited jaw opening, anxiety and stress) after 3 months. Comparing the efficiency of the procedures after 3 months between the two groups, awake bruxism and perceived stress are significantly different. (4) Conclusions: Although the differences are not radical when comparing MT with MT+C at three months, the patients who received either manual therapy or this treatment combination showed an improvement in pain relief, in the frequency and complexity of their symptoms, a reduction in functional disability and an overall improvement of the quality of their lives after three months of treatment.