The need for promoting scientific literacy for all students has been the focus of recent education reform resulting in the rise of the Science Technology, Engineering, and Mathematics movement. For students with Autism Spectrum Disorders and intellectual disability, this need for scientific literacy is further complicated by the need for individualized instruction that is often required to teach new skills, especially when those skills are academic in nature. In order to address this need for specialized instruction, as well as scientific literacy, this study investigated the effects of embedded computer-assisted instruction to teach science terms and application of those terms to three middle school students with autism and intellectual disability. This study was implemented within an inclusive science classroom setting. A multiple probe across participants research design was used to examine the effectiveness of the intervention. Results of this study showed a functional relationship between the number of correct responses made during probe sessions and introduction of the intervention. Additionally, all three participants maintained the acquired science terms and applications over time and generalized these skills across materials and settings. The findings of this study suggest several implications for practice within inclusive settings and provide suggestions for future research investigating the effectiveness of computer-assisted instruction to teach academic skills to students with Autism Spectrum Disorders and intellectual disability.