The recent discovery of a Plasmodium parasite in the endangered Galapagos Penguin (Spheniscus mendiculus) poses a threat to the long-term persistence of this endangered species and, potentially, much of the endemic avifauna of the Galapagos Islands. However, little information is available on the transmission dynamics or pathogenicity of Plasmodium in the Galapagos. We added a simple model of infection to the population model of the Galapagos Penguin devised by Vargas et al. (2007). Two variables (the probability of an individual becoming infected each year, and the increase in annual mortality caused by infection) define the dynamics of the disease component of the model; the stress from El Niño events could affect parasitized individuals in different ways, so three forms of stress-induced relapse are also explored. All models show a high impact due to mortality from infection, and there are large parts of parameter space that have a 0% probability of persistence for the next 100 years. To estimate the mortality that might be associated with Plasmodium infection, a comparison was made between census data from 1998–2009 and model predictions based on the same years. A range of plausible mortality values was determined from the best-fitting models, ranging from 0–5% to 0–10% depending on the type of relapse modeled. Even at these relatively low levels of impact, Plasmodium infection has the potential to drastically reduce the probability of persistence of the Galapagos Penguin population over the next 100 years.