Geographical variations in stroke incidence and case-fatality have been documented worldwide. This study examines whether there are spatio-temporal variations in stroke incidence and case-fatality in Hong Kong and attempts to determine to what extent socioeconomic status (SES) and healthcare provision account for these variations. Residence-based hospital discharge data from the Hospital Authority (HA) in Hong Kong were geo-referenced and used to examine incidence rates and case-fatality rates by stroke subtype among the population aged 35 years and above in 1999-2007. Multilevel models were used to examine the spatio-temporal variations. Ischemic stroke incidence was found to decrease among those aged above 55 years, while hemorrhagic stroke incidence increased. Ischemic stroke case-fatality was found to decrease but hemorrhagic stroke case-fatality remained stable. For both subtypes, there were significant variations in stroke incidence and case-fatality across the districts of residence, but insignificant variations across HA service clusters. Only variations in ischemic stroke incidence and hemorrhagic stroke case-fatality at the district level could be partly explained by district-level SES. Identification of districts with higher risk for stroke incidence and case-fatality would help to formulate enhanced preventive measures. Future studies are needed to identify factors that contribute to the geographical variations.