Temporomandibular disorder (TMD) is an umbrella term including pain problems involving the cranio-cervical region. It has been suggested that patients with TMD also exhibit cervical spine disturbances. Evidence suggests the presence of morphological changes in the deep cervical muscles in individuals with headaches. The objective of this study was to compare the morphology of the suboccipital muscles between women with TMD and healthy controls. An observational, cross-sectional case-control study was conducted. An ultrasound examination of the suboccipital musculature (rectus capitis posterior minor, rectus capitis posterior major, oblique capitis superior, oblique capitis inferior) was conducted in 20 women with myofascial TMD and 20 matched controls. The cross-sectional area (CSA), perimeter, depth, width, and length of each muscle were calculated by a blinded assessor. The results revealed that women with myofascial TMD pain exhibited bilaterally reduced thickness, CSA, and perimeter in all the suboccipital muscles when compared with healthy women. The width and depth of the suboccipital musculature were similar between women with myofascial TMD and pain-free controls. This study found morphological changes in the suboccipital muscles in women with myofascial TMD pain. These changes can be related to muscle atrophy and are similar to those previously found in women with headaches. Future studies are required to investigate the clinical relevance of these findings by determining if the specific treatment of these muscles could help clinically patients with myofascial TMD.