In our previous project, an XML-based authoring tool was provided for teachers to script multimedia teaching material with animated agents, and a stand-alone learning system was designed for students to display the material and interact with animated agents. We also provided evidence that the authoring tool and learning system in computer-assisted learning systems successfully enhances learning performance. The aim of this study is to continue the previous project, to develop a Web-based multimedia learning system that presents materials and an animated agent on a Web browser. The Web-based multimedia learning system can provide an opportunity for students to engage in independent learning or review of school course work. In order to demonstrate the efficiency of this learning system, it was applied to one elementary school. An experimental material, `Road Traffic Safety', was presented in two learning systems: a Web-based PowerPoint learning system and a Web-based multimedia learning system. The experiment was carried out in two classes that had a total of thirty-one 3rd-grade students. The results suggest that using our authoring tool in a Web-based learning system can improve learning, and in particular, enhance learners' problem-solving ability. Students with higher achievement on the post-test showed better comprehension in problem-solving questions. Furthermore, the feedback from the questionnaire surveys show students' learning interest can be fostered when an animated agent is integrated into multimedia teaching materials, and that students prefer to adopt the Web-based multimedia learning system for independent learning after school.