The purpose of this study is to design of a Web Based Mathematics Teaching System (WBMTS) for teaching of probability unit and to implement and evaluate its effectiveness on 10th grade students learning these unit subjects of mathematics. In accordance with this aim, WBMTS was designed and piloted for the teaching of permutation-combination-binomial expansion and probability subjects of mathematics course. As a result of this pilot study the WBMTS was reorganized and revised as a final form. The study was conducted during spring semester of 2008-2009 academic years in a high school in Trabzon, Turkey. The sample of the study consists of ten teachers and seventy 10th grade students. Through mixed methods study the quantitative and qualitative data were gathered from the sample. In order to research the effect of the WBMTS on academic achievement of the students, experimental and control groups were formed using quasi-experimental method and one teacher in sample taught the control and experimental groups at the high school where the main study was conducted. The quantitative data obtained the study were analyzed by means of covariance analysis (ANCOVA). When the results of the research are observed, it is seen that the WBMTS has a positive effect on students' academic achievement. However, the results of the study showed that the use of WBMTS in teaching of this unit's subjects supports traditional classroom training mathematics.