This article discusses the relationship between the theory of Louis Althusser concerning the subjectivity of knowledge and the cognitive process and the effective use of educational computer simulations during Science Education and Science Teaching. Our first aim is to highlight the aspects of the cognitive process – according to Louis Althusser’s theory – that should be considered by teachers when they opt to utilize computer simulations in their classroom teaching in the subject of Science and Physics. Our second aim is to suggest ways in order to overcome the conceptual ambiguity, the misunderstandings and the misconceptions that sometimes students form while using simulation models on the computer. The research question being investigated here is the following: “What kind of learning outcomes might the use of computer simulations have concerning the acquisition and construction knowledge by students in the course of Science and Physics in the light of L. Althusser’s theory and what could teachers do so as to eliminate the potential risks of their use and to achieve better outcomes in the learning procedure?”. The utilization of computer simulations in Science Teaching sometimes make students think that the simulated object or phenomenon is identical in nature with the real one. However, the simulations do not constitute the “real objects” themselves; in contrary, they are the means to come closer to reality in order to study it thoroughly.