A modelling approach is used for studying the effects of population vaccination on the epidemic dynamics of a set of n cities interconnected by a complex transportation network. The model is based on a sophisticated mover-stayer formulation of inter-city population migration, upon which is included the classical SIS dynamics of disease transmission which operates within each city. Our analysis studies the stability properties of the Disease-Free Equilibrium (DFE) of the full n-city system in terms of the reproductive number R(0). Should vaccination reduce R(0) below unity, the disease will be eradicated in all n-cities. We determine the precise conditions for which this occurs, and show that disease eradication by vaccination depend on the transportation structure of the migration network in a very direct manner. Several concrete examples are presented and discussed, and some counter-intuitive results found.