Myofascial pain in the masticatory region, generally referred to as headache, is a common temporomandibular disorder (TMD) characterized by the hypersensitive regions of the contracted skeletal muscle fibers. A correct clinical treatment of myofascial pain has the potential to modify the functional activation of cerebral networks associated with pain and unconscious teeth clenching, specifically the pain network (PN) and default mode network (DMN). In this study, research is presented as a case series of five patients with myofascial pain: three were diagnosed with intra- and extra-articular disorders, and two were diagnosed with only extra-articular disorders. All five patients received gnathological therapy consisting of passive splints and biofeedback exercises for tongue–palatal vault coordination. Before and after treatment, patients underwent pain assessments (through measures of visual analog scales and muscular palpation tests), nuclear magnetic resonance of the temporomandibular joint, and functional nuclear magnetic resonance of the brain. In each patient, temporomandibular joint nuclear magnetic resonance results were similar before and after the gnathological treatment. However, the treatment resulted in a considerable reduction in pain for all patients, according to the visual analog scales and the palpation test. Furthermore, functional nuclear magnetic resonance of the brain clearly showed a homogeneous modification in cerebral networks associated with pain (i.e., PN and DMN), in all patients. In conclusion, gnathological therapy consisting of passive aligners and biofeedback exercises improved myofascial pain in all five patients. Most importantly, this study showed that all five patients had a homogeneous functional modification of pain and default mode networks. Using passive splints in combination with jaw exercises may be an effective treatment option for patients with TMD. This research could be a starting point for future investigations and for clinicians who want to approach similar situations.