In this paper we present an evolutionary variational inequality model of vaccination strategies games in a population with a known vaccine coverage profile over a certain time interval. The population is considered to be heterogeneous, namely its individuals are divided into a finite number of distinct population groups, where each group has different perceptions of vaccine and disease risks. Previous game theoretical analyses of vaccinating behaviour have studied the strategic interaction between individuals attempting to maximize their health states, in situations where an individual’s health state depends upon the vaccination decisions of others due to the presence of herd immunity. Here we extend such analyses by applying the theory of evolutionary variational inequalities (EVI) to a (one parameter) family of generalized vaccination games. An EVI is used to provide conditions for existence of solutions (generalized Nash equilibria) for the family of vaccination games, while a projected dynamical system is used to compute approximate solutions of the EVI problem. In particular we study a population model with two groups, where the size of one group is strictly larger than the size of the other group (a majority/minority population). The smaller group is considered much less vaccination inclined than the larger group. Under these hypotheses, considering that the vaccine coverage of the entire population is measured during a vaccine scare period, we find that our model reproduces a feature of real populations: the vaccine averse minority will react immediately to a vaccine scare by dropping their strategy to a nonvaccinator one; the vaccine inclined majority does not follow a nonvaccinator strategy during the scare, although vaccination in this group decreases as well. Moreover we find that there is a delay in the majority’s reaction to the scare. This is the first time EVI problems are used in the context of mathematical epidemiology. The results presented emphasize the important role played by social heterogeneity in vaccination behaviour, while also highlighting the valuable role that can be played by EVI in this area of research.