Background: Onabotulinumtoxin A (OBT-A) is a treatment option for chronic migraine (CM), though the possible effect on central sensitization and allodynia is still unknown. Aims: The present study aimed to evaluate (1) the long-term outcome of allodynia in a group of CM treated with OBT-A (2) if the presence and severity of allodynia could predict the long-term effect of OBT-A (3) if the improvement of allodynia, could contribute to the clinical efficacy of OBT-A. Methods: This was an observational, open-label, cohort study conducted on 99 CM patients treated for 1 year and 44 patients treated for 2 years with periodic OBT-A 155–195 U injections. In basal condition (T0), after 1 year (T1) and 2 years (T2) treatment, allodynia, migraine disability, and headache frequency were the main variables. Anxiety, depression and sleep deprivation were also considered potentially correlated factors to allodynia. Results: Allodynia decreased after 1 year (Student t test p = 0.0001), and decreased further after the second year of treatment (p = 0.015). There was a relationship between allodynia severity at T0 and reduced headache frequency change at T1 (r = 0.22) and T2 (r = 0.37). The effect of OBT-A on allodynia correlated with the reduction of MIDAS score after 1 year (r = 0.4) and 2 years (r = 0. 63) of treatment. Conclusions: OBT-A seems to have an effect on central sensitization, expressed by allodynia. This action could be exerted by modulating nociceptive transmission, and reducing the global burden of migraine. Patients with more severe allodynia display a limited long-term effect on headache frequency. The modulation of central sensitization could reduce migraine disability, in spite of the persistence of frequent headache.