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Abstract This paper demonstrates how two different methods used to calculate population-level mobility from Call Detail Records (CDR) produce varying predictions of the spread of epidemics informed by these data. Our findings are based on one CDR dataset describing inter-district movement in Ghana in 2021, produced using two different aggregation methodologies. One methodology, “all pairs,” is designed to retain long distance network connections while the other, “sequential” methodology is designed to accurately reflect the volume of travel between locations. We show how the choice of methodology feeds through models of human mobility to the predictions of a metapopulation SEIR model of disease transmission. We also show that this impact varies depending on the location of pathogen introduction and transmissibility. For central locations or highly transmissible diseases, we do not observe significant differences between aggregation methodologies on the predicted spread of disease. For less transmissible diseases or those introduced into remote locations, we find that the choice of aggregation methodology influences the speed of spatial spread as well as the size of the peak number of infections in individual districts. Our findings can help researchers and users of epidemiological models to understand how methodological choices at the level of model inputs may influence the results of models of infectious disease transmission, as well as the circumstances in which these choices do not alter model predictions. Author Summary Predicting the sub-national spread of infectious disease requires accurate measurements of inter-regional travel networks. Often, this information is derived from the patterns of mobile device connections to the cellular network. This travel data is then used as an input to epidemiological models of infection transmission, defining the likelihood that disease is “exported” between regions. In this paper, we use one mobile device dataset collected in Ghana in 2021, aggregated according to two different methodologies which represent different aspects of inter-regional travel. We show how the choice of aggregation methodology leads to different predicted epidemics, and highlight the conditions under which models of infection transmission may be influenced by methodological choices in the aggregation of travel data used to parameterize these models. For example, we show how aggregation methodology changes predicted epidemics for less-transmissible infections and under certain models of human movement. We also highlight areas of relative stability, where aggregation choices do not alter predicted epidemics, such as cases where an infection is highly transmissible or is introduced into a central location.