Nowadays, studying prehistoric sites in Indonesia has become convenient because of the touch of technology. We no longer need to spend money, time, and energy to visiting the sites in person. Virtual Reality (VR) is the commonly used immersive technology for virtualizing prehistoric sites. Cutting-edge research is utilizing Virtual Reality (VR) technology to construct virtual environments of prehistoric sites, allowing people to learn and enjoy them with flexibility. However, in the context of learning, its use is still quite limited due to general features. Therefore, it is necessary to develop applications with more complete and interactive learning features. The aim of this study is to develop a web-based Si-VirPraJa (Prehistoric Virtual Site) application. We employed research and development (R&D) to achieve the objectives of the research. Furthermore, we used the ADDIE development model, which includes analysis, design, development, implementation, and evaluation. We initiated the research by conducting a needs analysis study of the Si-VirPraJa App as expected by students and teachers. The needs analysis results formed the foundation for designing the application’s initial stage. Learning media experts tested it and provided assessments, suggestions, and comments. The Si-VirPraJa app, refined based on assessment results, suggestions, and comments from media experts, is implemented in a trial class to gather feedback from students and teachers. The findings suggested that students need a virtual tour-based application to study prehistoric sites in Indonesia. This necessary application must also include multiple features that facilitate learning. The findings from validation tests conducted by experts and trials class that the Si-VirPraJa application is viable for use as a learning media. The impact of using this application for learning is evident in students’ enhanced self-learning ability, improved comprehension of the material, and the generation of engaging and meaningful learning experiences.