Microgrids have received much attention in recent years because of its potential to deliver economic, social, technical and environmental benefits. However, its implementation has major challenges in different areas to make them viable, such as control, energy management, and the development of protection schemes. The latter has several issues still to be resolved. In fact, in literature, several authors propose methods to deal with such issues, highlighting those aimed for a centralized protection system with an adaptive strategy. The challenges of protection systems relate to the incorporation of distributed generation from renewable sources and its intermittence, as well as the ability to operate in both connected mode and islanded mode, which involves continuous change of operation, among others. This article reviews in detail the challenges to be addressed in developing microgrid protection schemes, together with the analysis of a real case such as the Huatacondo microgrid, in northern Chile.