The availability of cost-effective and environmentally friendly electricity to the entire population is a prime concern of the South African government. It has brought attention to microgrid projects, especially when rural population is considered properly. To address the energy needs of any country, the focus line should be the cost and availability of local resources. Due to the abundance of coal reserves and lack of alternative resources, coal dependence cannot be overlooked in the near future. This paper focuses not only on microgrid needs in South Africa but also on the possible use of hydrogen extracted from coal as a fuel in Proton Exchange Membrane Fuel Cell (PEMFC) in microgrids. The complete assembly of PEMFC and its use in the microgrid are discussed. To make the H2 extraction process eco-friendly and hence worth considering, Carbon capture and sequestration process is discoursed. Furthermore, cost benefit analysis and the long term benefit of the use of PEMFC in microgrids with coal-based hydrogen production are presented in this research.