The aim of this paper is to study the stochastic monotonicity and continuity properties of the extinction time of Bellman-Harris branching processes depending on their reproduction laws. Moreover, we show their applications in an epidemiological context, obtaining an optimal criterion to establish the proportion of susceptible individuals in a given population that must be vaccinated in order to eliminate an infectious disease. First the spread of infection is modelled by a Bellman-Harris branching process. Finally, we provide a simulation-based method to determine the optimal vaccination policies.