The objective of this work was to investigate the association between the function of the stomatognathic system and migraine presence through an instrumental functional analysis in a group of diagnosed migraine patients and a control group. This study included 50 individuals in each group. A jaw-tracking analysis was performed using Cadiax 4. Tracings of the following movements were recorded: open/close, protrusion/retrusion, mediotrusion, speech, bruxing, and mastication. The tracings were evaluated for their quantity, quality, transversal characteristics, speed, curvature pattern, and condylar stability. Statistically significant differences between the groups were established for several aspects of the evaluation. Migraineurs presented with (a) higher values of mandibular lateral translation in protrusion/retrusion (p = 0.001), open/close (p = 0.031), and mastication (p = 0.016); (b) transient velocity losses in open/close (p = 0.001) and protrusive movements (p = 0.018); (c) a compromised condylar stability for protrusion/retrusion (p = 0.001) and mediotrusion (p = 0.003); (d) a compromised quality for protrusion/retrusion (p < 0.001) and mediotrusion (p = 0.003); and (e) a more frequent "figure-eight" curvature in open/close (p = 0.012). The importance of the stomatognathic function in migraine pathogenesis and treatment should be considered by using a patient-centered and interdisciplinary approach.