Scientific reasoning is particularly pertinent to science education since it is closely related to the content and methodologies of science and contributes to scientific literacy. Much of the research in science education investigates the appropriate framework and teaching methods and tools needed to promote students' ability to reason and evaluate in a scientific way. This paper aims (a) to contribute to an extended understanding of the nature and pedagogical importance of model-based reasoning and (b) to exemplify how using computer simulations can support students' model-based reasoning. We provide first a background for both scientific reasoning and computer simulations, based on the relevant philosophical views and the related educational discussion. This background suggests that the model-based framework provides an epistemologically valid and pedagogically appropriate basis for teaching scientific reasoning and for helping students develop sounder reasoning and decision-taking abilities and explains how using computer simulations can foster these abilities. We then provide some examples illustrating the use of computer simulations to support model-based reasoning and evaluation activities in the classroom. The examples reflect the procedure and criteria for evaluating models in science and demonstrate the educational advantages of their application in classroom reasoning activities.