This paper presents an entirely new approach to the use of virtual reality (VR) in the educational process for the needs of Industry 4.0. It is based on the proposed comprehensive methodology, including the design, creation, implementation and evaluation of individual courses implemented in a VR environment. An essential feature of the new methodology is its universality and comprehensiveness. Thanks to that, it can be applied in such areas as higher education, aviation, automotive, shipbuilding, energy and many others. The paper also identifies the significant advantages and disadvantages of VR-based education that may determine its use scope and profile. In addition, on the basis of the proposed methodology, a model of a training station using VR technology has been developed to enable the realization of training classes in the field of firefighting activities that should be undertaken during the hazard arising from the operation of a numerically controlled production machine. Results of the conducted training using this station were also presented. The study showed the potential of training based on a virtual environment to improve participants’ skills and knowledge. The development and implementation of adequate courses in the VR environment can reduce costs and increase the safety and efficiency of employees’ performed activities.