The treatment of a complex temporomandibular disorder (TMD), such as disk displacement with reduction (DDR) associated with arthralgia and myalgia, may depends on understanding the impairments in muscle function. The aim of this study was to investigate the behavior of the anterior temporalis, masseter and sternocleidomastoid muscles in the time and frequency domains during chewing in patients with chronic painful TMD-DDR using electromyographic (EMG) analysis. Thirty-three patients who met the diagnostic criteria for TMD and 32 volunteers without TMD (control group) underwent clinical examination, chewing pattern classification and EMG analysis. For the EMG analyses, the side of habitual unilateral chewing, as determined by the chewing pattern classification, was selected for recording; in cases of bilateral chewing, the recording side was randomly selected. The EMG-EMG coherence function and EMG-EMG transfer function (gain and phase) values were obtained at the first chewing frequency peak, and the working-side masseter signal was used as a reference in the analyses of the other muscles. Compared to the control group, the TMD group showed a longer chewing stroke duration (P = 0.01) as well as changes in the coactivation and coordination strategies of the jaw muscles, evidenced by greater relative energy expenditure (P< 0.01) and impaired differential recruitment (P< 0.05) and coherence (P< 0.01). Delays in peak and temporal asynchrony occurred in the jaw and neck muscles (P< 0.05). Patients with chronic painful TMD-DDR during chewing presented changes in the jaw and neck muscles, with more compromised function of the former, which are specific to chewing.