Coexistence of temporomandibular joint discomfort along with cervical spine disorders is quite common, and is associated with many limitations and adverse symptoms for the patient. Both diagnostics and treatment of these ailments are difficult, and in many cases, the effects of therapy are not satisfactory. This study assessed the impact of a 3-week neck-only rehabilitation programme without direct intervention in the craniofacial area on the bioelectric activity of both the cervical spine and muscles in the craniofacial area among patients with idiopathic neck pain who do not report TMJ pain. A parallel group trial with follow-up; Setting: Rehabilitation Clinic. Twenty five patients experiencing idiopathic neck pain underwent the 3-week rehabilitation programme. Thirty five age-matched subjects with no cervical spine and temporomandibular joint (TMJ) dysfunctions were control group. At baseline and after 3 weeks the cervical and craniofacial area muscles' bioelectrical activity (sEMG) was evaluated. In the experimental group during cervical flexion, a significant decrease of sEMG amplitude was noted in the right (mean 25.1 μV; 95% CI: 21.5-28.6 vs mean 16.8 μV; 95% CI: 13.8-19.7) and left (mean 25.9 μV; 95% CI: 21.7-30.0 vs mean 17.2 μV; 95% CI: 13.6-20.7) Sternocleidomastoid as well as a significant increase in sEMG amplitude of the right (mean 11.1 μV; 95% CI: 7.9-14.2 vs mean 15.7 μV; 95% CI: 12.1-19.2) and left (mean 15.3 μV; 95% CI: 11.9-18.6 vs mean 20.2 μV; 95% CI: 15.7-24.2) Upper Trapezius muscles. In the experimental group, after therapy right and left Sternocleidomastoid, Temporalis Anterior and Masseter muscles presented lower fatigue levels. Three weeks of rehabilitation without any therapeutic intervention in temporomandibular joint significantly decreased the bioelectrical activity of the neck and craniofacial muscles while improving the muscle pattern of coactivation in participants with idiopathic neck pain who do not report temporomandibular joint pain. These observations could be helpful in the physiotherapeutic treatment of neck and craniofacial area dysfunctions. ID ISRCTN14511735-retrospectively registered.