While computer simulations are a key element in understanding and doing science today, their nature and implications for science education have not been adequately explored in the relevant literature. In this article, (1) we provide an analysis of the methodology and epistemology of computer simulations, aiming to contribute to a sound and comprehensive account of the nature of computer simulations in science education, and (2) examine certain implications for science education, particularly in terms of contemporary educational goals relating to scientific literacy. We describe methodological elements relating to processes, techniques, and skills required for the construction and evaluation of scientific simulations, and we discuss epistemological views of their reliability and epistemic status based on the relevant philosophical views. We then examine implications of these elements for the use of simulations and especially for supporting scientific practices in the classroom and the corresponding educational goals. Concretely, we compare educational simulations with those used in scientific research and with laboratory experiments, we discuss the question of the reliability of simulations used in teaching or in public information, and we give examples of their use for supporting NOS understanding and reasoning abilities. Finally, in the context of the philosophical discourse about scientific realism, we examine implications of the epistemology of models that concern the conception of the relation between scientific claims and the real world, which constitutes a fundamental epistemological basis for teaching the nature of science.