A stack structure of a fuel cell according to an aspect of the invention includes a plurality of separators of the fuel cell, and a protruding portion which has a tip portion that contacts a reference portion of an assembly jig during assembly of the fuel cell. Since the tip portion of the protruding portion contacts the reference portion of the assembly jig, an adhesive agent does not come out from the tip portion of the protruding portion. Therefore, it is possible to prevent positioning accuracy in stacking cells from being reduced. The reduction of the positioning accuracy is due to adhesion of the spreading adhesive agent to the reference portion of the assembly jig. In addition, it is possible to prevent a short-circuit from occurring. The occurrence of the short-circuit is due to deformation of the separator caused by making the separator contact the reference portion of the assembly jig.