Solar energy plays an important role in the global energy framework for future. Comparing with conventional generation systems using fossil fuels, the cost structure of photovoltaic (PV) systems is different: the capital cost is higher while the operation cost is negligible. Reliabilities of the PV system can also influence the cost for producing electricity. Investors, planners and regulators require deep insight into the return and cost of a PV project. A reliability based economical assessment of large-scale PV systems has been conducted utilizing Universal Generating Function (UGF) techniques. The reliability models of solar panel arrays, PV inverters and energy production units (EPUs) are represented as the corresponding UGFs. The expected energy production models for different PV system configurations have also been developed. The expected unit cost of electricity has been calculated to provide informative metrics for making optimal decisions. The proposed method has been applied to determine the PV system configuration which provides electricity for a water purification process.