The availability of water and the ability to access are the key questions arising in developing countries including Jordan, which is the fourth poorest country in the world regarding water resources. Renewable energy, especially solar energy, can potentially play a role in the supply of safe water in Jordan Badia, where nearly 80% of the total area of Jordan is Badia, and in most cases these deep wells are far away from the national grid electricity, and in some of these areas there is an important quantity of groundwater at shallow depths. This paper introduces and compares the cost-effectiveness and the Present Value Cost (PVC) for the economic evaluation of power supply for pumping systems in remote areas in Northern Badia of Jordan by two different energy supply systems, photovoltaic systems and diesel engines. Many variables are taken into account such as the fuel prices, and the required investments. The comparison is made for a wide range of variable values, total head, tank capacity, photovoltaic array peak power and pumping requirements. A case study in Tall Hassan station is conducted to analyze the two power supply pumping systems, which are designed to supply drinking water. The results obtained are useful for choosing the best alternative for the power supply of pumping systems in wells in Northern Badia of Jordan.