Greece, along with most of the countries in the Mediterranean basin, is historically linked with forest fires. Wildfires have always occurred, are happening, and will continue to occur, causing serious problems regarding the sustainability of natural resources. Their frequency, however, has shown a noticeable increase during the last decades; according to the most recent projections, the broader Mediterranean region will face significant challenges in the future within the context of climate change. Despite the historical experience of forest fires in Greece, a standardized and up-to-date system for identifying and prioritizing burnt areas, in relation to their restoration needs, has not yet been developed and adopted. In this paper, a systematic methodological approach for decision-making regarding the identification and prioritization of active restoration/reforestation of burnt areas is proposed. This approach is based on critical parameters, such as the regeneration potential of the affected forest species, the “fire history”, and the slope of the affected areas. The proposed methodological approach can be applied in all burnt natural areas in the country in the future, as well as in other areas of the Mediterranean region. The fire impact on Natura 2000 sites is also assessed to highlight the importance of restoration and conservation needs in protected areas. The results from case studies are presented, and future steps and policy recommendations for the post-fire management of natural ecosystems are discussed to enable the sustainable management of forest resources in the burnt areas.