This article discusses the integration of animated pedagogical agent into the development of cognitive tools based upon Scientific Inquiry Model for invoking learners? cognitive conflict and fostering conceptual change. In this study, animated pedagogical agent acts as a catalyst while coaching the learner who interacts individually carrying out the hypothesize-observe-experiment activities. Study shows that through cognitive apprenticeship, the animated pedagogical agent is able to interact actively with the learners by allowing them to make their own sense of imposed ideas, extracting meaningful patterns and integrating new input with their prior belief and ideas in order to foster the conceptual change process.