Although it is essential to shorten the interval to initial treatment in the care of acute ischemic stroke, some hospitals in Japan reject requests for hospital acceptance from on-scene emergency medical service personnel because of limited resources, which can cause delays in care. We aimed to assess the risk factors for difficulty of hospital acceptance of patients suspected to have cerebrovascular diseases. We conducted a retrospective analysis of the national ambulance records of the Fire and Disaster Management Agency in Japan in 2016. Multivariable logistic regression analysis was used to assess the association between difficulty of hospital acceptance of patients suspected to have cerebrovascular diseases and prehospital factors. During the study period, a total of 222,926 patients were included, and 5283 patients (2.4%) experienced difficulties in hospital acceptance. In multivariable analysis, nights (adjusted odds ratio [AOR] 1.54, 95% confidence interval [CI] 1.45–1.64), weekends (AOR 1.32, 95% CI 1.24–1.40), <25 percentile ratio of emergency physicians and neurosurgeons to all physicians (AOR 1.13, 95% CI 1.03–1.23) (AOR 1.36, 95% CI 1.25–1.48), and mean age of physicians (AOR 1.06, 95% CI 1.05–1.07) were significantly associated with difficulties of hospital acceptance of patients suspected to have cerebrovascular disease. There was a marked regional variation in the difficulties of hospital acceptance. Among the national ambulance records of patients suspected to have cerebrovascular diseases, certain prehospital factors such as weekends were positively associated with difficulty of hospital acceptance. A comprehensive strategy for hospital acceptance of patients with cerebrovascular diseases considering regional variation is required.