Headaches, especially migraines, have been associated with various vestibular symptoms and syndromes. Tinnitus and hearing loss have also been reported to be more prevalent among migraineurs. However, whether headaches, including migraine or non-migraine headaches (nMH), are associated with vestibular and cochlear disorders remains unclear. Thus, we sought to investigate possible associations between headache and vestibulocochlear disorders. We analyzed 10 years of data from the Smart Clinical Data Warehouse. In patients with migraines and nMH, meniere’s disease (MD), BPPV, vestibular neuronitis (VN) and cochlear disorders, such as sensorineural hearing loss (SNHL) and tinnitus, were collected and compared to clinical data from controls who had health check-ups without headache. Participants included 15,128 with migraines, 76,773 patients with nMH and controls were identified based on propensity score matching (PSM). After PSM, the odds ratios (OR) in subjects with migraine versus controls were 2.59 for MD, 2.05 for BPPV, 2.98 for VN, 1.74 for SNHL, and 1.97 for tinnitus, respectively (p < 0.001). The OR for MD (1.77), BPPV (1.73), VN (2.05), SNHL (1.40), and tinnitus (1.70) in patients with nMH was also high after matching (p < 0.001). Our findings suggest that migraines and nMH are associated with an increased risk of cochlear disorders in addition to vestibular disorders.