A method of operating a fuel cell system including: a reducing agent supplier for supplying a reducing agent; an oxidizing agent supplier for supplying an oxidizing agent; a fuel cell main body including plural cells stacked, the cells being each provided with a reducing agent passage and an oxidizing agent passage which are isolated by an MEA having a polymer electrolyte membrane as a base material; a reducing agent supply path to which reducing agent supply ends which are end portions of reducing agent passages of all of the cells are connected; an oxidizing agent supply path to which oxidizing agent supply ends which are end portions of oxidizing agent passages of all of the cells are connected; and a water supplier for supplying water to at least one of the reducing agent supply path and the oxidizing agent supply path; wherein each of the plural cells includes a pair of separators, each of which is provided with a groove-shaped reducing agent passage and a groove-shaped oxidizing agent passage, the reducing agent supply path includes a pipe member and a reducing agent supply manifold, the oxidizing agent supply path includes a pipe member and an oxidizing agent supply manifold, a reducing agent discharge path is connected to a discharge end of the reducing agent passage, an oxidizing agent discharge path is connected to a discharge end of the oxidizing agent passage, the reducing agent discharge path includes a pipe member and a reducing agent discharge manifold, and the oxidizing agent discharge path includes a pipe member and an oxidizing agent discharge manifold, characterized in that said method comprises: in a start-up operation of the fuel cell system, a water layer forming step in which before starting supply of at least one of the reducing agent and the oxidizing agent in a supply start operation of at least one of the reducing agent and the oxidizing agent, the water supplier supplies water to form a water layer so as to clog at least one of at least a portion of the reducing agent supply path which is located upstream of the reducing agent supply end in a flow direction of the reducing agent and at least a portion of the oxidizing agent supply path which is located upstream of the oxidizing agent supply end in a flow direction of the oxidizing agent, wherein in the water layer forming step, a water supply pressure and a water supply time of the water supplied from the water supplier are respectively a water supply pressure and a water supply time with which the water does not pass through all of reducing agent passages and all of oxidizing agent passages. a reducing agent supplier for supplying a reducing agent; an oxidizing agent supplier for supplying an oxidizing agent; a fuel cell main body including plural cells stacked, the cells being each provided with a reducing agent passage and an oxidizing agent passage which are isolated by an MEA having a polymer electrolyte membrane as a base material; a reducing agent supply path to which reducing agent supply ends which are end portions of reducing agent passages of all of the cells are connected; an oxidizing agent supply path to which oxidizing agent supply ends which are end portions of oxidizing agent passages of all of the cells are connected; and a water supplier for supplying water to at least one of the reducing agent supply path and the oxidizing agent supply path; wherein in a start-up operation of the fuel cell system, a water layer forming step in which before starting supply of at least one of the reducing agent and the oxidizing agent in a supply start operation of at least one of the reducing agent and the oxidizing agent, the water supplier supplies water to form a water layer so as to clog at least one of at least a portion of the reducing agent supply path which is located upstream of the reducing agent supply end in a flow direction of the reducing agent and at least a portion of the oxidizing agent supply path which is located upstream of the oxidizing agent supply end in a flow direction of the oxidizing agent, a water layer forming step in which before starting supply of at least one of the reducing agent and the oxidizing agent in a supply start operation of at least one of the reducing agent and the oxidizing agent, the water supplier supplies water to form a water layer so as to clog at least one of at least a portion of the reducing agent supply path which is located upstream of the reducing agent supply end in a flow direction of the reducing agent and at least a portion of the oxidizing agent supply path which is located upstream of the oxidizing agent supply end in a flow direction of the oxidizing agent,