This paper proposes a benefit of the doubt (BoD) approach to assess the research performance of 37 public Australian universities based on data from 2015. The primary activities of Higher Education institutions are teaching and research, but the prestige of a university depends mainly on the results of its research activities. The BoD method is rooted in the data envelopment analysis methodology, which enables the flexible and data-based assignment of weights to aggregated variables. Full weighting flexibility, however, allows zero weights, which can lead to unrealistic results. For this reason, the proposed model has been supplemented with additional weight restrictions. The assessment considers key performance factors: number of publications and citations; number of completed doctoral degrees; amount of research grants; and percentage of science graduates. Unlike earlier research on Australian universities, this study uses the number of publications and citations from the Web of Science database. The results provide a ranking of universities and recommendations for decision makers regarding the direction of future improvement actions for the worst-performing universities.