Background Functional magnetic resonance is a non-invasive method that can examine brain activity and has been widely used in various fields including jaw movement and pain processing. Temporomandibular disorder (TMD) is one of the most frequent facial pain problems. The objective of this study was to investigate the brain activities using functional magnetic resonance imaging (fMRI) during unilateral maximal voluntary clenching tasks in the TMD synovitis patients with biting pain.Methods Fourteen TMD synovitis patients with unilateral biting pain and 14 controls were included in the study.Contralateral biting pain was defined as right molar clenching causing left temporomandibular joint (TMJ) pain. Ipsilateral biting pain was defined as right molar clenching causing right TMJ pain. Symptom Check List-90 (SCL-90) was administered to the patients and controls. Independent sample t-test was used to compare the SCL-90 subscales between the two groups. Unilateral clenching tasks were performed by the patients and controls. Imaging data were analyzed using SPM99.Results Patients were divided into contralateral TMD biting pain group (n=8) and ipsilateral TMD biting pain group (n=6). The SCL-90 subscales were significantly different between the two groups for somatization, depression, anxiety,phobic anxiety, and paranoid ideation. Group analysis of the controls demonstrated brain activations in the inferior frontal gyrus, precentral gyrus, middle frontal gyrus, superior temporal gyrus, and insular. The areas of activation were different between right and left clenching task. In TMJ synovitis patients with contralateral or ipsilateral biting pain, the group analysis showed activations in the inferior frontal gyrus, superior temporal gyrus, medium frontal gyrus, precentral gyrus,and anterior cingulate cortex.Conclusions The inferior frontal gyrus and precentral gyrus play essential roles during the unilateral clenching task.Activation of anterior cingulate cortex in the synovitis patients with biting pain was associated with higher levels of psychological distress.