(1) Background: Vestibular migraine (VM) and Menière’s disease (MD) share multiple features in terms of clinical presentations and auditory-vestibular functions, and, therefore, more accurate diagnostic tools to distinguish between the two disorders are needed. (2) Methods: The study was of retrospective design and examined the data of 69 MD patients, 79 VM patients and 72 MD with migraine patients. Five vestibular autorotation test (VAT) parameters, i.e., horizontal gain/phase, vertical gain/phase and asymmetry were subjected to logistic regression. The receiver operating characteristic (ROC) curves were generated to determine the accuracy of the different parameters in the differential diagnosis of MD and VM. (3) Results: Our results showed that the horizontal gain of VAT significantly outperformed other parameters in distinguishing MD and VM. In addition, the sensitivity, specificity and accuracy of the horizontal gain were 95.7%, 50.6% and 71.6%, respectively, for the differentiation between VM and MD. In most MD patients, the horizontal gain decreased in the range of 3–4 Hz, while in most VM patients, horizontal gain increased in the range between 2–3 Hz. More MD with migraine patients had an increased horizontal gain when the frequency was less than 5.0 Hz and had a decreased horizontal gain when the frequency was greater than 5.0 Hz. (4) Conclusion: Our study suggested the VAT, especially the horizontal gain, as an indicator, may serve as a sensitive and objective indicator that helps distinguish between MD and VM. Moreover, VAT, due to its non-invasive and all-frequency nature, might be an important part of a test battery.