The subjective visual vertical (SVV) test has been frequently used to measure vestibular contribution to the perception of verticality. Recently, mobile devices have been used to efficiently perform this measurement. The aim of this study was to analyze the perception of verticality in subjects with migraines and headaches. A cross-sectional study was conducted that included 28 patients with migraine, 74 with tension-type headache (TTH), and 93 healthy subjects. The SVV test was used through a new virtual reality system. The mean absolute error (MAE) of degrees deviation was also measured to qualify subjects as positive when it was greater than 2.5°. No differences in the prevalence of misperception in verticality was found among healthy subjects (31.18%), migraineurs (21.43%), or those with TTH (33.78%) (p = 0.480). The MAE was not significantly different between the three groups (migraine = 1.36°, TTH = 1.61°, and healthy = 1.68°) (F = 1.097, p = 0.336, and η2 = 0.011). The perception of verticality could not be explained by any variable usually related to headaches. No significant differences exist in the vestibular contribution to the perception of verticality between patients with headaches and healthy subjects. New tests measuring visual and somatosensory contribution should be used to analyze the link between the perception of verticality and headaches.