Musculoskeletal (MSK) disorders are some of the most burdensome health issues in the world and the leading causes of years living with a disability. Between them, jaw pain and neck have been very prevalent among the general population. Subjects with chronic neck and jaw pain present with persistent pain, allodynia, and hyperalgesia, sometimes extending to regions distant from the neck, head, or face, as well as cognitive and motor dysfunction. In addition, both conditions are commonly related to pain in other anatomical regions, and they also might also exhibit a greater risk for pain-associated somatic symptom burden. The treatment for patients with neck and jaw could involve different techniques in the rehabilitation area. Between them, therapeutic exercise is a cornerstone of MSK disease rehabilitation. Although mechanisms of action for exercise in subjects with pain are not yet understood, therapeutic exercise is widely applied in a variety of painful MSK conditions, such as low back pain, shoulder pain, knee pain, osteoarthritis, and disorders of the cervical and craniofacial regions such as temporomandibular disorders, headaches, and neck pain. Besides its effects on function and health, therapeutic exercise is known to have some pain-relieving effects and specific motor control exercises targeted to the neck can enhance the neural control of the cervical spine in patients with neck involvement such as patients with jaw and neck pain. Previous studies have demonstrated that treatment directed to the neck may be beneficial in decreasing pain intensity in the masticatory muscles, increasing pain-free mouth opening, and decreasing pain in the head and neck regions in people with jaw pain. In addition, neck motor control exercises have been successful to manage chronic neck pain and cervicogenic headache. Subjects with neck pain and associated disorders receiving neck motor control exercises had a reduction of pain and improved quality of life. Another option that has been explored to relieve MSK pain is aerobic exercise. Aerobic exercise has been used to stimulate the release of pain-relieving peptides in healthy human beings; however, little is known about the analgesic effect of exercise in people suffering from actual musculoskeletal pain. Previous literature found positive results in favor of aerobic exercise for pain relief. However, none of them included patients with jaw and neck-related disorders. Therefore, the aim of the present pilot randomized controlled trial (RCT) is to test the effectiveness of local craniocervical motor control exercises when compared with aerobic exercise on pain-disability related outcomes such as pain intensity, pain pressure thresholds (PPTs), jaw and neck disabilities and to restore normal muscular performance and fatigability of the cervical muscles in people with jaw and neck pain. Also, an important objective for performing this pilot study is to test the feasibility of these protocols and gather data that will be the basis for applying to external funding. This study will be a randomized controlled trial, blinded, two-armed parallel group. It will include women between 18-60 years of age; diagnosed with temporomandibular disorders (i.e., jaw pain) classified by the new Diagnostic Criteria for Temporomandibular Disorders (DC/TMD); or diagnosed with idiopathic chronic neck pain associated or not with TMD. Because this is an exploratory (pilot) study it will include at least 21 subjects per treatment group. The primary outcome will be pain intensity evaluated by the Visual Analogue Scale (VAS), and the secondary outcomes will be Neck Disability Index; Jaw Function; Pressure Pain Threshold; Psychological functioning; Global Rating Scale; and Muscular performance and fatigability of the cervical muscles. The patients will be randomized into two groups: local craniocervical motor control exercises and aerobic exercise. The local craniocervical motor control exercises program will be focused on training the deep and superficial flexors and extensors neck muscles. The treatment will consist of a 12-week progressive training program with a total duration of 30-45 min per session. Individuals assigned to the aerobic exercise will receive cycling exercise, with a total duration of 60 minutes. Both groups will be evaluated before the treatment starts (baseline); after two and six weeks from the beginning of treatment (1st and 2nd partial evaluation); at the end of the treatment (final evaluation - 12 weeks); and after three and six months of the end of the treatment (1st and 2nd follow-up).