In this paper we investigate regional mortality and health status in Greece, using data from the European Statistical Office (Eurostat) for the period 1990–2020. Firstly, a logistic function is fitted to the data series of each period life table, in order to estimate and smooth the age specific death rate in older ages. Using these age-specific death rates and through a dynamic model with stochastic simulation, we estimate the health state function across the 13 regions of Greece for each year of study and sex. Through the parameters of the health state function, we estimate the median age at death and the total health state for the population of each life table. Furthermore, a hierarchical cluster analysis is performed on the results of the previous analysis in order to determine possible groupings in the regions of study. The results show an overall increasing of the median lifetime and total health state in Greece, but with significant regional and gender variations. Finally, the study offers interesting results for the mortality and health status during the Greek economic crisis and the subsequent austerity measures (2008–2015).