Pupils with learning impediments in elementary schools have difficulties in learning numerical calculations. Numerical concepts, the basis of numerical calculations, require repetitious exercises, and it has been widely reported that computer-mediated learning motivates the learners to concentrate on their learning for longer hours. The aim of the research is to develop and apply a Web-based courseware to experimental groups to improve learning numerical concepts of the learners with learning difficulties in elementary school and to discuss the effects of the results. The courseware is designed to improve the numerical concepts of the learners through many thought activities. The experiment shows effectiveness of the learning activities to improve learning numerical concepts for students with learning difficulties, categorized into two groups - an experimental group and a control group, and also it shows positive responses on improvement of their calculation ability.