Temporomandibular disorders (TMD), characterized by pain and dysfunction of the temporomandibular joint, are the most common chronic orofacial pain. However, the etiologies and pathologies of TMD related chronic pain are poorly understood. Functional magnetic resonance imaging (fMRI) measures brain activity by detecting changes associated with blood flow without invasiveness, and has been widely used in chronic pain research. We reviewed recent fMRI studies exploring the brain changes of patients with painful TMD to investigate the role of central nervous system in abnormal pain perception and impaired pain modulation, and to summarize the effects of splint therapy, in the hope of facilitating the clinical diagnosis and treatment of TMD.