Pathological changes of the lateral pterygoid muscle (LPM) have been investigated using various modalities, including magnetic resonance (MR) imaging and electromyography. Fluid-attenuated inversion recovery (FLAIR) is an MR sequence that we hypothesized can be used to evaluate abnormalities of the LPM. The purpose of this study was to analyze the FLAIR signal intensity of the LPM in painful temporomandibular joints (TMJs) and investigate the pathological changes of the muscle. The study was based on 149 TMJs of 77 patients who were referred for MR imaging of the TMJ. Patients rated their degree of pain during chewing and mouth opening using a visual analog scale (VAS). Regions of interest were placed over the superior and inferior heads of the LPM and gray matter on FLAIR sagittal images. Using the signal intensity of gray matter as a reference, the signal intensity ratio (SIR) of the LPM was calculated. Spearman's rank-correlation coefficient was used to analyze the correlation between the SIR and the VAS score (p < 0.05). A significant correlation was present between the SIR on FLAIR images and the VAS score. These results suggest that the FLAIR signal intensity of the superior and inferior heads of the LPM significantly increases as TMJ pain becomes more severe. Thus, FLAIR could be useful in assessing the relationship between the MR signals of the LPM and clinical symptoms.