Nowadays, environmental issues are greatly concerned. Conventional solutions that use lead acid batteries and diesel engines as sources of energy for both uninterruptible power supply (UPS) and isolated power generation systems are facing an increasing opposition due to environmental and economical concerns. The aim of the paper is to evaluate the technical feasibility and aspects related to the use of fuel cells instead of traditional electrochemical batteries in the UPS. The proposed system is named FCB-UPS (Fuel Cell Based UPS). However, the quality of UPS output voltage is important when it supports the sensitive loads. So, in this paper a new configuration of UPS based on flying capacitor multicell (FCM) converter is proposed to produce the multilevel output voltage to support the sensitive load with sinusoidal voltage. The main properties of FCM converter, which causes increase in the number of output voltage levels, are transformer-less operation and natural self-balancing of flying capacitors voltages. The proposed configuration is simulated using PSCAD/EMTDC software and simulation results are presented to validate its effectiveness.